{"gene":"TP53BP1","run_date":"2026-04-28T21:42:59","timeline":{"discoveries":[{"year":2001,"finding":"53BP1 becomes hyperphosphorylated and forms discrete nuclear foci in response to DNA damage; ATM-deficient cells show no 53BP1 hyperphosphorylation and reduced foci formation; 53BP1 is phosphorylated by ATM in vitro, establishing 53BP1 as an ATM substrate in DNA damage signaling.","method":"Immunofluorescence, in vitro kinase assay, ATM-deficient cell lines, wortmannin inhibition","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro kinase assay plus genetic (ATM-deficient cells) and pharmacological validation, replicated across labs","pmids":["11331310"],"is_preprint":false},{"year":2001,"finding":"53BP1 localizes to chromatin and forms nuclear foci upon DNA damage; Xenopus 53BP1 is hyperphosphorylated after X-ray irradiation in an ATM kinase-dependent manner; inhibitors of ATM-related kinases delay relocalization and reduce phosphorylation of 53BP1.","method":"Live cell imaging, immunofluorescence, X-irradiation, ATM kinase inhibitors, AT cells","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — genetic and pharmacological evidence in Xenopus and human AT cells, consistent with PMID:11331310","pmids":["11238909"],"is_preprint":false},{"year":2003,"finding":"A region upstream of the 53BP1 C-terminus is required and sufficient for recruitment to DNA break sites by directly binding phosphorylated H2AX (γH2AX) but not unphosphorylated H2AX; H2AX phosphorylation at serine 140 is critical for 53BP1 foci formation; ATM-mediated N-terminal phosphorylation of 53BP1 is not required for its relocalization.","method":"In vitro binding assay, H2AX-deficient cell reconstitution with wild-type or phospho-deficient H2AX, domain mapping","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro binding assay plus genetic reconstitution with phospho-deficient mutant","pmids":["12697768"],"is_preprint":false},{"year":2008,"finding":"53BP1 facilitates long-range DNA end-joining during V(D)J recombination; 53BP1-deficient lymphocytes show impaired distal V-DJ joining with extensive degradation of unrepaired coding ends, demonstrating a role in genomic stability during long-range joining of DNA breaks distinct from classical NHEJ.","method":"53BP1 knockout mouse model, V(D)J recombination assay, genomic analysis of TCR locus","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular and molecular phenotype","pmids":["18931658"],"is_preprint":false},{"year":2008,"finding":"53BP1 and MDC1 interact directly through the tandem BRCT domain of MDC1 and residues 1288–1409 of 53BP1; this interaction is required for recruitment of 53BP1 to DSB sites; after DSB induction, the interaction is reduced due to competition between γH2AX and 53BP1 for MDC1 BRCT domain binding; the interaction is enhanced during mitosis in a phospho-dependent manner.","method":"Co-IP, pulldown, domain mapping, immunofluorescence in H2AX-deficient and MDC1-deficient cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP with domain mapping and functional validation in relevant cell lines","pmids":["18986980"],"is_preprint":false},{"year":2009,"finding":"PTIP regulates 53BP1 localization to DNA damage sites downstream of RNF8; PTIP depletion prevents 53BP1 foci formation; SMC1 phosphorylation at DSB sites is dependent on PTIP, placing PTIP between RNF8 and 53BP1 in the DNA damage signaling pathway.","method":"siRNA knockdown, co-IP, immunofluorescence, epistasis analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis by siRNA with defined pathway placement; single lab","pmids":["19414588"],"is_preprint":false},{"year":2009,"finding":"Protein phosphatase 5 (PP5) binds 53BP1 and dephosphorylates it at Ser-25 and Ser-1778 after DNA damage; PP5 overexpression accelerates 53BP1 dephosphorylation and reduces phospho-53BP1 foci; PP5 downregulation inhibits dephosphorylation, prolonging foci; PP5 overexpression reduces NHEJ activity.","method":"Yeast two-hybrid, co-IP, overexpression/knockdown in U2OS cells, NHEJ reporter assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 — yeast two-hybrid plus co-IP and functional assay; single lab","pmids":["19176521"],"is_preprint":false},{"year":2010,"finding":"TopBP1 colocalizes with 53BP1 at DSBs in G1 phase; TopBP1 BRCT domains 4-5 interact with 53BP1; recruitment of TopBP1 to DSBs in G1 is dependent on 53BP1; loss of TopBP1 or 53BP1 causes G1 DNA damage checkpoint defects.","method":"Co-IP, siRNA knockdown, immunofluorescence, G1 checkpoint assay (S-phase entry after irradiation)","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — reciprocal interaction plus epistatic checkpoint phenotype","pmids":["20871591"],"is_preprint":false},{"year":2011,"finding":"53BP1 facilitates joining of intrachromosomal DSBs only at distances corresponding to γH2AX spreading (~1 Mb); DNA end protection by 53BP1 is distance-independent; chromatin association, oligomerization, and N-terminal ATM phosphorylation of 53BP1 are all required for DNA end protection and CSR.","method":"Paired DSB joining assay across chromosomal distances, 53BP1 mutant analysis, class switch recombination assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — multiple 53BP1 structural mutants tested with quantitative joining and CSR assays","pmids":["21549309"],"is_preprint":false},{"year":2011,"finding":"MMSET (NSD2/WHSC1) is recruited to DSBs via the γH2AX-MDC1 pathway (MDC1 BRCT domain binds phospho-Ser102 of MMSET) and locally methylates H4K20 at DSBs; this local increase in H4K20me2 is required for 53BP1 recruitment; MMSET knockdown significantly decreases H4K20me2 at DSBs and subsequent 53BP1 accumulation.","method":"ChIP, siRNA knockdown, co-IP, immunofluorescence, H4K20 methylation assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (ChIP, co-IP, KD) in a single study with clear mechanistic pathway","pmids":["21293379"],"is_preprint":false},{"year":2013,"finding":"53BP1 promotes productive CSR and suppresses mutagenic DNA repair through distinct phosphodependent interactions: ATM-mediated phosphorylation of S/TQ sites recruits RIF1 (via 8 N-terminal sites) for end-blocking, while separate phosphorylation recruits PTIP for CSR; a 53BP1-8A phosphomutant recruits RIF1 but not PTIP.","method":"53BP1 phosphomutant knock-in mice, CSR assay, immunofluorescence, co-IP","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1-2 — phosphomutant knock-in with multiple functional readouts (CSR, NHEJ, HR) and interactor recruitment","pmids":["23727112"],"is_preprint":false},{"year":2013,"finding":"53BP1 phase separates to form liquid-like repair compartments at DSBs; 53BP1 assembly is sensitive to osmotic pressure, temperature, salt, and hydrophobic interactions; p53 is enriched within 53BP1 optoDroplets; disruption of 53BP1 phase separation impairs p53 induction and p53 target gene expression.","method":"Live cell microscopy, CRISPR endogenous tagging, optoDroplet experiments, osmotic/chemical perturbations","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including optoDroplet, live imaging, and functional p53 readout","pmids":["31267591"],"is_preprint":false},{"year":2013,"finding":"RNF168 mediates K63-linked ubiquitylation of 53BP1, which is required for initial recruitment of 53BP1 to DSBs and for its function in DNA repair, checkpoint activation, and genomic integrity.","method":"Ubiquitylation assay, co-IP, RNF168 KO/KD cells, immunofluorescence","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — biochemical ubiquitylation assay plus functional validation in KO cells","pmids":["24324146"],"is_preprint":false},{"year":2013,"finding":"H4K16 acetylation antagonizes 53BP1 binding to H4K20me2; DNA damage induces transient, localized H4 deacetylation at DSBs which facilitates 53BP1 foci formation and NHEJ; 53BP1 foci assemble primarily on H4K20me2 established by SETD8 and SUV420 methyltransferases, not de novo MMSET-mediated methylation.","method":"Chromatin fractionation, siRNA knockdown of methyltransferases/HDAC, NHEJ reporter, immunofluorescence","journal":"Journal of molecular cell biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple knockdowns with functional assay; single lab","pmids":["23329852"],"is_preprint":false},{"year":2014,"finding":"53BP1 tandem Tudor domain binds methylated K810 of pRb; structural elucidation reveals recognition of the methylated lysine and surrounding residues; 53BP1 binding to methyl-K810 pRb occurs at E2F target genes, integrating pRb activity with the DNA damage response.","method":"Structural biology (crystal structure), binding assay, ChIP","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus functional ChIP validation","pmids":["25049398"],"is_preprint":false},{"year":2014,"finding":"UbcH7 (Ube2L3) regulates steady-state and replication stress-induced ubiquitination and proteasome-dependent degradation of 53BP1; N-terminal phosphorylation of 53BP1 is involved in replication stress-induced degradation; UbcH7 depletion stabilizes 53BP1, inhibits DSB end resection, increases NHEJ and decreases HR.","method":"shRNA screen, ubiquitination assay, NHEJ/HR reporter, immunoprecipitation","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2-3 — shRNA screen plus biochemical and functional validation; single lab","pmids":["25422456"],"is_preprint":false},{"year":2014,"finding":"ATM-dependent MOF phosphorylation at T392 colocalizes with 53BP1 at DSBs; MOF-T392A mutation blocks reduction of DSB-associated 53BP1 in S/G2 phase, enhances 53BP1 and reduces BRCA1 at DSBs, and impairs HR repair.","method":"Phospho-mutant expression, immunofluorescence, co-IP, HR reporter assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2-3 — phosphomutant with HR assay and localization data; single lab","pmids":["24953651"],"is_preprint":false},{"year":2015,"finding":"Chemical proteomics identified 53BP1 as a direct γH2AX binder through its BRCT domains; a 53BP1 mutant deficient in γH2AX binding shows altered localization to chromosomal breaks, revealing that direct γH2AX recognition by the BRCT domains modulates 53BP1 localization at damage sites.","method":"Quantitative chemical proteomics (γH2AX affinity pulldown from native proteome), mutant localization assay","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1-2 — native proteome pulldown plus mutagenesis with functional localization readout","pmids":["26344695"],"is_preprint":false},{"year":2015,"finding":"BRCA1 inhibits ATM-dependent 53BP1 phosphorylation in S/G2 phases, restricting RIF1 and PTIP accumulation at DSBs to G1; both BRCT and RING domains of BRCA1 are required for inhibition of 53BP1 phosphorylation, ensuring HR predominates in S/G2.","method":"Cell cycle-sorted cells, phospho-specific antibodies, immunofluorescence, BRCA1 domain mutants","journal":"Cell discovery","confidence":"Medium","confidence_rationale":"Tier 2-3 — domain mutant analysis with cell cycle-specific phosphorylation readout; single lab","pmids":["27462418"],"is_preprint":false},{"year":2016,"finding":"Cryo-EM structure of dimerized human 53BP1 bound to H4K20me2- and H2AK15ub-containing nucleosome (NCP-ubme) at 4.5 Å; reveals simultaneous engagement of H4K20me2 by tandem Tudor domain and H2AK15ub by UDR motif; ubiquitin is sandwiched between UDR and NCP surface; two arginine fingers in H2A tail position ubiquitin and confer selectivity for H2AK15ub over H2AK13ub; intimate contacts with the nucleosomal acidic patch are required.","method":"Cryo-EM structure determination at 4.5 Å, biochemical validation","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with mechanistic detail of dual histone mark recognition","pmids":["27462807"],"is_preprint":false},{"year":2016,"finding":"Silencing 53BP1 or exhausting its chromatin-binding capacity switches DSB repair from error-free gene conversion (RAD51) to mutagenic single-strand annealing (RAD52), demonstrating that 53BP1 fosters fidelity of HDR rather than simply suppressing it.","method":"siRNA knockdown, HR sub-pathway reporter assays, RAD51/RAD52 focus formation","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 — multiple HR sub-pathway reporters plus focus formation; single lab","pmids":["27348077"],"is_preprint":false},{"year":2017,"finding":"TIRR directly binds the tandem Tudor domain of 53BP1 and masks its H4K20me2 binding motif, preventing 53BP1 recruitment to DSBs; ATM phosphorylation of 53BP1 after DNA damage recruits RIF1 and dissociates the 53BP1-TIRR complex; TIRR overexpression impedes 53BP1 function; TIRR depletion destabilizes soluble 53BP1.","method":"Co-IP, pulldown, immunofluorescence, ATM inhibition, Tudor domain binding competition assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP, competition binding, multiple functional readouts; single lab with comprehensive validation","pmids":["28241136"],"is_preprint":false},{"year":2017,"finding":"Crystal structure of TIRR in complex with 53BP1 tandem Tudor domain at 1.76 Å; N-terminal region (residues 10-24) and L8-loop of TIRR interact with 53BP1 Tudor through loops L1, L3, and L1'; TIRR histidine H106 is essential for 53BP1 Tudor binding; TIRR recognition blocks H4K20me2 binding.","method":"X-ray crystallography, NMR, mutagenesis, in vivo functional assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — atomic resolution crystal structure with mutagenesis and functional validation","pmids":["29844495"],"is_preprint":false},{"year":2017,"finding":"NMR and biochemistry reveal that RNF169 bridges ubiquitin and histone surfaces on NCP-ubme with high affinity (conformational selection), displacing low-affinity 53BP1 from H2AK15ub nucleosomes; RAD18 also binds NCP-ubme through a ubiquitin-binding domain that contacts sites accessed by 53BP1, providing an alternative mechanism for 53BP1 displacement.","method":"NMR spectroscopy, biochemical binding assay, competition assays with reconstituted nucleosomes","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 — NMR plus reconstitution assays with mechanistic detail","pmids":["28506460"],"is_preprint":false},{"year":2017,"finding":"53BP1 accumulation at DSBs declines as cells progress through S phase due to replication-coupled dilution of H4K20me2; premature maturation of post-replicative chromatin restores H4K20me2 and rescues 53BP1 accumulation, establishing that H4K20me2 availability controls 53BP1-mediated repair pathway choice across the cell cycle.","method":"Live cell imaging, cell cycle synchronization, H4K20me2 ChIP, EdU labeling","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — ChIP and live imaging with mechanistic rescue experiment","pmids":["28564601"],"is_preprint":false},{"year":2017,"finding":"An engineered ubiquitin variant (i53) blocks 53BP1 accumulation at DSBs by inhibiting its UDR/Tudor-mediated chromatin recruitment, increasing HDR-dependent genome editing by up to 5.6-fold, confirming that 53BP1 suppresses end resection as a key step in HDR.","method":"Ubiquitin variant library screen, CRISPR-Cas9 HDR assay, immunofluorescence","journal":"Nature biotechnology","confidence":"High","confidence_rationale":"Tier 2 — biochemical screen plus functional HDR assay; mechanistic inhibitor study","pmids":["29176614"],"is_preprint":false},{"year":2018,"finding":"Shieldin complex (SHLD1/C20orf196, SHLD2/FAM35A, SHLD3/CTC-534A2.2, REV7) is a 53BP1 effector that localizes to DSBs in a 53BP1- and RIF1-dependent manner; SHLD2 binds single-stranded DNA via OB-fold domains; loss of shieldin impairs NHEJ, immunoglobulin class switching, causes hyper-resection, and confers PARP inhibitor resistance in BRCA1-deficient cells.","method":"Proteomics/MS, co-IP, genetic KO, immunofluorescence, ssDNA binding assay, CSR assay, PARPi sensitivity","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1-2 — complex identified by MS, validated by co-IP and KO, with multiple functional assays; replicated in concurrent studies","pmids":["30022168"],"is_preprint":false},{"year":2018,"finding":"CST (CTC1-STN1-TEN1) interacts with shieldin downstream of 53BP1-RIF1; CST and Polα localize to DNA damage sites in a 53BP1- and shieldin-dependent manner; CST-Polα-mediated fill-in controls DSB repair by limiting resection; CST depletion increases resection and, in BRCA1-deficient cells, blocks RAD51 loading and diminishes PARPi efficacy.","method":"Co-IP, immunofluorescence, siRNA knockdown, resection assays, RAD51 focus formation, PARPi sensitivity","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP plus multiple functional assays; mechanistic fill-in model tested with Polα inhibition","pmids":["30022158"],"is_preprint":false},{"year":2018,"finding":"53BP1 cooperates with REV7 to promote NHEJ during CSR, while REV7 is dispensable for 53BP1-dependent V(D)J recombination; shieldin (REV7-SHLD1-SHLD2-SHLD3) explains this DNA structure specificity by mediating end-protection in ssDNA compartments and is essential for REV7-dependent NHEJ in CSR but dispensable for REV7-dependent interstrand crosslink repair.","method":"Mouse genetics (conditional KO), CSR assay, V(D)J recombination analysis, shieldin identification by proteomics","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1-2 — multiple KO mouse models plus proteomics identification; independent replication by concurrent shieldin papers","pmids":["30046110"],"is_preprint":false},{"year":2018,"finding":"DYNLL1 directly binds 53BP1 and stimulates 53BP1 oligomerization, promoting 53BP1 recruitment and interaction with DSB-associated chromatin; loss of DYNLL1 or its transcriptional regulator ASCIZ impairs CSR and renders BRCA1-mutant tumors resistant to PARP inhibitors.","method":"Co-IP, pulldown, immunofluorescence, DYNLL1 KO mice, CSR assay, PARPi sensitivity assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — co-IP plus multiple functional assays in KO cells/mice","pmids":["30559443"],"is_preprint":false},{"year":2018,"finding":"CBP-mediated acetylation of 53BP1 at K1626/K1628 in the UDR motif disrupts interaction between 53BP1 and nucleosomes, blocking recruitment of 53BP1, PTIP, and RIF1 to DSBs and shifting repair toward HR; HDAC2 reverses this acetylation to maintain NHEJ/HR balance.","method":"Co-IP, immunofluorescence, acetylation assay, NHEJ/HR reporter, HDAC2 knockdown","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2-3 — biochemical acetylation assay plus functional reporters; single lab","pmids":["29190394"],"is_preprint":false},{"year":2018,"finding":"GFI1 interacts with PRMT1 and enables PRMT1 to bind and methylate 53BP1 (and MRE11), which is necessary for 53BP1 function in the DNA damage response; GFI1 deletion causes hypersensitivity to ionizing radiation and DNA repair defects.","method":"Co-IP, methylation assay, GFI1 KO, immunofluorescence, clonogenic survival","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2-3 — co-IP plus methylation assay and KO phenotype; single lab","pmids":["29651020"],"is_preprint":false},{"year":2019,"finding":"53BP1 enforces two distinct anti-HR blocks: (1) a pre-resection block via PTIP interaction (S25 phosphorylation site) controlling DNA2-dependent end resection, and (2) a post-resection block via shieldin that inhibits RNF168-mediated PALB2/RAD51 loading onto ssDNA.","method":"53BP1-S25A knock-in mice crossed with BRCA1Δ11 mice, RAD51/PALB2 focus formation, PARPi sensitivity, epistasis analysis","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 — knock-in mice with multiple orthogonal mechanistic readouts and epistasis","pmids":["31653568"],"is_preprint":false},{"year":2019,"finding":"53BP1 nuclear bodies (53BP1-NBs) in G1 daughter cells restrain replication of embedded under-replicated DNA loci until late S phase, enabling RAD52-mediated repair; absence or malfunction of 53BP1-NBs causes premature replication of affected loci and genotoxic RAD51-mediated recombination.","method":"Live cell imaging, CRISPR labeling, EdU incorporation, RAD52/RAD51 focus assay, replication timing analysis","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 — live imaging plus genetic manipulation with specific replication timing and repair pathway readouts","pmids":["30804506"],"is_preprint":false},{"year":2019,"finding":"TOPBP1 BRCT domains selectively bind conserved phosphorylation sites in the N-terminus of 53BP1; mutation of these sites abolishes TOPBP1, ATR, and CHK1 recruitment to 53BP1 damage foci and abrogates G1 cell cycle arrest; TOPBP1 interaction with 53BP1 is structurally complementary to its interaction with RAD9-RAD1-HUS1, allowing simultaneous binding and cooperation in ATR activation.","method":"Structural analysis, phospho-mutant analysis, co-IP, G1 checkpoint assay, immunofluorescence","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1-2 — structural data plus phospho-mutant functional analysis with ATR signaling readout","pmids":["31135337"],"is_preprint":false},{"year":2019,"finding":"TPX2/Aurora A heterodimer is a novel 53BP1 binding partner; TPX2/Aurora A counteracts 53BP1 function to promote DNA end resection, BRCA1/Rad51 recruitment, and HR; loss of TPX2 or Aurora A causes deprotection of stalled replication forks in an MRE11-dependent manner; concurrent 53BP1 loss rescues BRCA1/Rad51 recruitment and fork instability.","method":"Co-IP (MS), immunofluorescence, siRNA knockdown, replication fork protection assay, HR assay","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — MS-based co-IP plus functional rescue by 53BP1 loss; single lab","pmids":["30602538"],"is_preprint":false},{"year":2019,"finding":"LC8 (DYNLL1) accumulates at laser-induced DNA damage tracks in a 53BP1-dependent manner, requiring the H2AX-MDC1-RNF8-RNF168 cascade; genetic inactivation of LC8 or its interaction with 53BP1 causes checkpoint defects; LC8 loss alleviates hypersensitivity of BRCA1-depleted cells to IR and PARP inhibition.","method":"Laser micro-irradiation, co-IP, LC8 genetic inactivation, checkpoint assay, PARPi sensitivity","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2-3 — localization plus genetic inactivation with checkpoint and PARPi readouts; single lab","pmids":["30982887"],"is_preprint":false},{"year":2019,"finding":"Preformed 53BP1 dimers relocate from the nucleoplasm to DSB sites; at DSBs, consecutive recognition of H2AK15ub and H4K20me2 leads to assembly of 53BP1 oligomers and a mature foci structure, as quantified in living cells by fluorescence fluctuation spectroscopy.","method":"Fluorescence fluctuation spectroscopy (FFS), AsiSI-inducible DSB system, live-cell imaging","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — quantitative live-cell method establishing oligomerization dynamics at endogenous DSBs","pmids":["33188174"],"is_preprint":false},{"year":2020,"finding":"53BP1 localizes to replication forks following induced replication stress and is required for normal ATR-Chk1-p53 signaling; absence of 53BP1 leads to defective ATR-Chk1 signaling, caspase 3-mediated cell death, and degradation of nascent replicated DNA in early S-phase B cells.","method":"53BP1-/- primary B cells, replication fork labeling (EdU/BrdU), Chk1 phosphorylation assay, caspase activation","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — KO primary cells with multiple mechanistic readouts; single lab","pmids":["29378830"],"is_preprint":false},{"year":2020,"finding":"PRMT5 methylates and stabilizes 53BP1 to promote NHEJ; Src kinase phosphorylates PRMT5 at Y324, suppressing PRMT5 methyltransferase activity and preventing 53BP1 methylation; Src-mediated inhibition of PRMT5 during DNA damage blocks NHEJ and leads to apoptosis.","method":"In vitro methylation assay, co-IP, phospho-mutant analysis, NHEJ reporter, apoptosis assay","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — in vitro methylation assay plus functional NHEJ assay; single lab","pmids":["32759981"],"is_preprint":false},{"year":2020,"finding":"NUDT16 regulates 53BP1 stability by reversing ADP-ribosylation; ADP-ribosylated 53BP1 is targeted by RNF146 for polyubiquitination and degradation; NUDT16 catalytic activity is required for 53BP1 de-ADP-ribosylation, stability, and localization at DSBs.","method":"ADP-ribosylation assay, ubiquitination assay, co-IP, NUDT16 catalytic mutant, immunofluorescence","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2-3 — biochemical modification assays plus localization functional readout; single lab","pmids":["31911551"],"is_preprint":false},{"year":2020,"finding":"Centrosome loss in neural progenitor cells prolongs mitosis and activates a 53BP1-USP28-TP53 mitotic surveillance pathway causing apoptosis; deletion of 53BP1 or USP28 restores NPC proliferation and brain size without correcting upstream centrosome defects, establishing 53BP1 as a required component of this pathway.","method":"Conditional KO mouse models, brain size measurement, mitotic timing assay, apoptosis assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis in multiple KO mouse models with clear developmental phenotype","pmids":["33226141"],"is_preprint":false},{"year":2021,"finding":"ATM-phosphorylated SPOP undergoes a conformational change (revealed by crystal structure) that stabilizes its interaction with 53BP1; SPOP induces polyubiquitination of 53BP1, causing VCP/p97-mediated extraction of 53BP1 from chromatin during S phase, thus promoting HR over NHEJ; cancer-derived SPOP mutations block this interaction.","method":"X-ray crystal structure of SPOP, co-IP, ubiquitination assay, SPOP mutant analysis, HR/NHEJ reporter","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1-2 — crystal structure plus biochemical ubiquitination/co-IP and functional HR assay","pmids":["34144977"],"is_preprint":false},{"year":2021,"finding":"AHNAK binds the 53BP1 oligomerization domain in G1 phase and controls 53BP1 multimerization; loss of AHNAK leads to hyper-accumulation of 53BP1 on chromatin and enhanced phase separation, culminating in elevated p53 response.","method":"Co-IP, fluorescence microscopy, phase separation assay, p53 target gene expression, siRNA/KO","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — co-IP with domain mapping plus phase separation and functional p53 readout","pmids":["33961796"],"is_preprint":false},{"year":2021,"finding":"TIRR inhibits formation of the 53BP1 Tudor domain-p53 K382me2 complex; loss of TIRR causes aberrant increases in p53 transactivation; TIRR binds the Tudor domain and blocks p53 dimethyl-lysine recognition, linking TIRR to cell-fate decisions beyond DSB repair.","method":"Co-IP, Tudor domain-p53 binding assay (methylated K382 peptide), p53 target gene expression, TIRR KO","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — biochemical binding assay plus functional gene expression readout and KO phenotype","pmids":["33961797"],"is_preprint":false},{"year":2021,"finding":"Lamin B1 directly interacts with 53BP1 and sequesters it from DSB sites; lamin B1 overexpression impedes 53BP1 recruitment to DNA damage, causes persistence of DNA damage, and defects in NHEJ; the interaction is dissociated after DNA damage.","method":"Co-IP, pulldown, immunofluorescence, NHEJ reporter, DSB sensitivity assay","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct co-IP plus functional NHEJ assay and localization; single lab","pmids":["34452908"],"is_preprint":false},{"year":2021,"finding":"AMPK directly phosphorylates 53BP1 at Ser1317 in response to DSBs; this phosphorylation promotes 53BP1 recruitment to DSBs and efficient classical NHEJ (c-NHEJ), maintaining genomic stability and immune repertoire diversity.","method":"In vitro kinase assay (AMPK-53BP1), co-IP, phospho-mutant analysis, immunofluorescence, CSR assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro kinase assay plus phospho-mutant functional analysis; single lab","pmids":["33596428"],"is_preprint":false},{"year":2021,"finding":"ATM phosphorylates ESCO2 at S196 and T233; MDC1 recognizes phosphorylated ESCO2 and recruits it to DSBs; ESCO2-mediated SMC3 acetylation stabilizes cohesin complex conformation and regulates chromatin structure at DSBs, which is essential for 53BP1 recruitment and formation of 53BP1 microdomains.","method":"Co-IP, acetylation assay, siRNA knockdown, immunofluorescence, ESCO2 KO cells/xenograft","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2-3 — co-IP plus biochemical acetylation and functional 53BP1 recruitment assay; single lab","pmids":["37377435"],"is_preprint":false},{"year":2022,"finding":"53BP1 undergoes liquid-liquid phase separation with HP1α at heterochromatin in a mutually dependent manner; 53BP1 deletion reduces heterochromatin centers and de-represses tandem repetitive DNA; domains required for LLPS at heterochromatin overlap with but are distinct from those for DSB repair.","method":"LLPS assay, CRISPR KO, immunofluorescence, repeat RNA expression assay, domain deletion analysis","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2-3 — LLPS assay plus KO phenotype and domain analysis; single lab","pmids":["35042897"],"is_preprint":false},{"year":2022,"finding":"RIF1 is a phosphopeptide-binding protein that directly interacts with three phosphorylated 53BP1 epitopes sharing an LxL motif followed by two closely apposed phosphorylated residues; simultaneous mutation of these sites abrogates RIF1 IRIF but only fully compromises repair when an alternative shieldin recruitment mode is also disabled; RIF1 also modifies shieldin action independently of 53BP1 binding.","method":"Phosphopeptide binding assay, mutagenesis, co-IP, immunofluorescence (IRIF), CSR assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 — phosphopeptide binding assay plus mutagenesis and functional assay revealing two RIF1 recruitment modes","pmids":["35216668"],"is_preprint":false},{"year":2023,"finding":"SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thereby reducing DNA repair at DSBs.","method":"SARS-CoV-2 infection of cells and mice, 53BP1 foci quantification, lncRNA perturbation assay","journal":"Nature cell biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — viral protein expression with 53BP1 foci readout and mechanistic lncRNA link; single lab","pmids":["36894671"],"is_preprint":false}],"current_model":"53BP1 is recruited to DNA double-strand break (DSB) sites through its tandem Tudor domain binding dimethylated H4K20 (H4K20me2) and its UDR motif binding RNF168-catalyzed H2AK15ub on nucleosomes (structural basis resolved by cryo-EM); ATM phosphorylates 53BP1 to recruit the downstream effectors RIF1 (via phosphopeptide recognition of LxL-phospho motifs) and PTIP (via distinct phospho-sites), and RIF1 in turn recruits the shieldin complex (SHLD1-SHLD2-SHLD3-REV7), whose SHLD2 subunit binds single-stranded DNA to protect DNA ends; CST-Polα acts downstream of shieldin to perform fill-in synthesis that limits resection; this entire 53BP1-RIF1-shieldin-CST/Polα axis suppresses 5′ end resection, promotes NHEJ and class switch recombination, and opposes homologous recombination, while BRCA1 antagonizes 53BP1 signaling in S/G2 by inhibiting ATM-dependent 53BP1 phosphorylation; 53BP1 chromatin access is additionally regulated by TIRR (which masks the Tudor domain), SPOP-mediated polyubiquitination (which extracts 53BP1 from chromatin in S phase), acetylation of the UDR motif by CBP/HDAC2, ADP-ribosylation reversed by NUDT16, and sequestration by lamin B1 and NuMA; beyond DSB repair, 53BP1 phase separation amplifies p53 signaling, 53BP1 nuclear bodies restrain replication timing of under-replicated DNA, and 53BP1 participates in the mitotic surveillance pathway (with USP28 and TP53) to eliminate cells after prolonged mitosis."},"narrative":{"teleology":[{"year":2001,"claim":"Establishing that 53BP1 is an ATM substrate that forms DNA-damage-induced nuclear foci answered the foundational question of how 53BP1 is activated in the damage response, placing it within the ATM signaling axis.","evidence":"Immunofluorescence, in vitro ATM kinase assay, ATM-deficient human cells and Xenopus extracts","pmids":["11331310","11238909"],"confidence":"High","gaps":["Downstream substrates/effectors of 53BP1 phosphorylation unknown","Whether foci formation requires direct chromatin binding or indirect recruitment unresolved"]},{"year":2003,"claim":"Demonstrating that 53BP1 recruitment depends on γH2AX identified the chromatin mark that seeds 53BP1 accumulation, resolving how the damage signal spreads to recruit repair factors.","evidence":"In vitro binding assay with phosphorylated/unphosphorylated H2AX; reconstitution in H2AX-deficient cells","pmids":["12697768"],"confidence":"High","gaps":["Whether γH2AX binding is direct via the BRCT domain versus indirect via MDC1 not yet distinguished","Tudor domain–histone methylation recognition not yet discovered"]},{"year":2008,"claim":"Knockout studies revealed that 53BP1 promotes long-range DNA end joining during V(D)J recombination and that MDC1 acts as an intermediary between γH2AX and 53BP1, defining 53BP1's physiological role in lymphocyte genome rearrangement.","evidence":"53BP1 KO mice with V(D)J joining defects; MDC1–53BP1 co-IP and recruitment epistasis in H2AX/MDC1-deficient cells","pmids":["18931658","18986980"],"confidence":"High","gaps":["Mechanism of DNA end protection unknown","Whether 53BP1 physically prevents resection or acts indirectly unresolved"]},{"year":2011,"claim":"Discovery that MMSET-deposited H4K20me2 at DSBs recruits 53BP1, together with the finding that oligomerization and ATM phosphorylation are both needed for CSR, established that 53BP1 uses a histone-methylation-reading mechanism distinct from γH2AX and that multiple 53BP1 features cooperate in repair.","evidence":"H4K20me2 ChIP at DSBs with MMSET knockdown; 53BP1 structural mutants tested in quantitative CSR and paired-DSB joining assays","pmids":["21293379","21549309"],"confidence":"High","gaps":["Whether H4K20me2 is read by the Tudor domain directly not structurally confirmed","Effector proteins downstream of 53BP1 phosphorylation not yet identified"]},{"year":2013,"claim":"Phosphomutant knock-in mice and biochemical studies separated 53BP1's effector arms: ATM-phosphorylated S/TQ sites recruit RIF1 for end-blocking while distinct sites recruit PTIP for productive CSR; concurrently, RNF168-catalyzed K63-ubiquitylation of 53BP1 was shown to be required for initial recruitment, and H4K16 acetylation was identified as an antagonist of H4K20me2 binding.","evidence":"53BP1 phosphomutant knock-in mice with CSR/NHEJ/HR readouts; RNF168 KO ubiquitylation assays; H4K16ac chromatin fractionation and NHEJ reporter","pmids":["23727112","24324146","23329852"],"confidence":"High","gaps":["Structural basis of dual histone-mark recognition unresolved","Identity of end-protection effectors downstream of RIF1 unknown"]},{"year":2016,"claim":"The cryo-EM structure of 53BP1 bound to ubiquitylated-methylated nucleosomes resolved the long-standing question of how 53BP1 simultaneously reads H4K20me2 (Tudor domain) and H2AK15ub (UDR motif), revealing selectivity determinants including arginine fingers and acidic-patch contacts.","evidence":"Cryo-EM at 4.5 Å of 53BP1 dimer on reconstituted NCP-ubme nucleosome","pmids":["27462807"],"confidence":"High","gaps":["How higher-order oligomerization relates to foci maturation not shown structurally","Mechanism by which BRCA1 displaces 53BP1 in S/G2 structurally unresolved"]},{"year":2017,"claim":"Multiple regulatory layers of Tudor domain access were uncovered: TIRR was identified as a Tudor-masking protein whose dissociation is ATM-dependent; H4K20me2 dilution during replication was shown to limit 53BP1 accumulation in S phase; and competitors RNF169/RAD18 were shown to displace 53BP1 from ubiquitylated nucleosomes.","evidence":"TIRR co-IP and competition binding; crystal structure of TIRR–Tudor complex at 1.76 Å; cell-cycle H4K20me2 ChIP with EdU; NMR of RNF169/RAD18–NCP-ubme competition","pmids":["28241136","29844495","28564601","28506460"],"confidence":"High","gaps":["Signal that releases TIRR in vivo not fully defined","Quantitative contribution of each gating mechanism to pathway choice not measured"]},{"year":2018,"claim":"The shieldin complex (SHLD1–SHLD2–SHLD3–REV7) and downstream CST–Polα were identified as the missing effectors that explain how 53BP1–RIF1 physically blocks end resection, with SHLD2 OB-folds binding ssDNA and Polα performing fill-in synthesis; loss of shieldin confers PARPi resistance in BRCA1-deficient cells.","evidence":"Proteomic identification; co-IP and genetic KO; ssDNA binding assays; CSR and PARPi sensitivity assays across multiple concurrent studies","pmids":["30022168","30022158","30046110"],"confidence":"High","gaps":["Structural basis of shieldin assembly and ssDNA engagement unknown at atomic level","Whether CST–Polα acts at all 53BP1-dependent repair events or only CSR unclear"]},{"year":2018,"claim":"Additional modulators of 53BP1 chromatin occupancy were defined: CBP acetylation of the UDR motif blocks nucleosome binding (reversed by HDAC2), DYNLL1 promotes 53BP1 oligomerization, and BRCA1 inhibits ATM-dependent 53BP1 phosphorylation in S/G2 to favor HR.","evidence":"Acetylation assay and NHEJ/HR reporters; DYNLL1 KO mice with CSR assay; cell-cycle-sorted phospho-specific IF with BRCA1 domain mutants","pmids":["29190394","30559443","27462418"],"confidence":"Medium","gaps":["How BRCA1 mechanistically inhibits ATM phosphorylation of 53BP1 remains unclear","Whether acetylation and DYNLL1 regulation are coupled not tested"]},{"year":2019,"claim":"53BP1 was shown to enforce two mechanistically separable anti-HR blocks (a pre-resection block via PTIP/S25 and a post-resection block via shieldin), and to form nuclear bodies in G1 daughters that restrain replication timing of under-replicated loci, revealing functions beyond acute DSB repair.","evidence":"53BP1-S25A knock-in × BRCA1Δ11 mice with epistasis; live-cell replication timing analysis of 53BP1-NB-associated loci","pmids":["31653568","30804506"],"confidence":"High","gaps":["How 53BP1-NBs sense under-replicated DNA is unknown","Whether the two anti-HR blocks are independently regulated in different tissues unclear"]},{"year":2019,"claim":"53BP1 liquid–liquid phase separation was shown to concentrate p53 and amplify its transcriptional response, establishing that 53BP1 foci are condensates with signaling function beyond structural scaffolding.","evidence":"OptoDroplet experiments, endogenous CRISPR tagging, osmotic/chemical perturbation, p53 target gene expression","pmids":["31267591"],"confidence":"High","gaps":["Which phase-separation-competent domains are essential in vivo unclear","Relationship between LLPS and chromatin-bound oligomers not mechanistically separated"]},{"year":2020,"claim":"53BP1 was placed in a mitotic surveillance pathway with USP28 and TP53 that eliminates neural progenitor cells after prolonged mitosis; NUDT16-mediated de-ADP-ribosylation was found to stabilize 53BP1 by preventing RNF146-dependent degradation.","evidence":"Conditional triple KO mice with brain size rescue; ADP-ribosylation/ubiquitination assays with NUDT16 catalytic mutants","pmids":["33226141","31911551"],"confidence":"High","gaps":["How 53BP1 senses prolonged mitosis mechanistically unresolved","Whether ADP-ribosylation regulates 53BP1 at DSBs or only governs steady-state levels unclear"]},{"year":2021,"claim":"Structural and biochemical work showed that SPOP phosphorylation by ATM induces conformational opening that enables 53BP1 polyubiquitination and VCP-mediated chromatin extraction in S phase; TIRR was further shown to block Tudor–p53-K382me2 recognition, linking TIRR to cell-fate signaling; AHNAK was identified as an oligomerization regulator controlling 53BP1 phase separation and p53 output.","evidence":"SPOP crystal structure, ubiquitination and HR assay; TIRR–Tudor–p53-K382me2 binding assay; AHNAK co-IP and phase separation assay","pmids":["34144977","33961797","33961796"],"confidence":"High","gaps":["Cancer-derived SPOP mutations' effects on 53BP1-dependent repair in patient tumors not validated","How AHNAK itself is regulated during DSB signaling unknown"]},{"year":2022,"claim":"The structural code for RIF1 recruitment was resolved: RIF1 is a phosphopeptide-binding protein recognizing three LxL-phospho motifs in 53BP1, with an alternative shieldin recruitment mode providing redundancy; 53BP1 was also shown to phase-separate with HP1α at heterochromatin to maintain repeat silencing.","evidence":"Phosphopeptide binding assay with mutagenesis and CSR; LLPS assay with CRISPR KO and repeat RNA expression","pmids":["35216668","35042897"],"confidence":"High","gaps":["Structural basis of full-length RIF1–53BP1 complex not determined","Whether heterochromatin LLPS function is independent of DSB repair in vivo unclear"]},{"year":null,"claim":"Key open questions include: the structural basis of 53BP1 higher-order oligomerization at DSBs; how 53BP1 senses prolonged mitosis in the surveillance pathway; whether distinct post-translational modifications (ADP-ribosylation, methylation, acetylation) cooperate or act in separate contexts; and the full mechanism by which BRCA1 inhibits ATM-dependent 53BP1 phosphorylation.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structure of full-length 53BP1 oligomer on chromatin","Mitotic surveillance sensing mechanism unknown","Integrated PTM code for 53BP1 not systematically tested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[9,13,14,19,24]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[10,26,27,32,49]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[0,1,37]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[19,24,42]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[33,48]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[3,8,10,19,26,27,32]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,10,28]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[7,34,41]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[41]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[19,48]}],"complexes":["53BP1-RIF1-shieldin (SHLD1-SHLD2-SHLD3-REV7)","53BP1-TIRR"],"partners":["RIF1","SHLD2","REV7","TIRR","DYNLL1","PTIP","TOPBP1","AHNAK"],"other_free_text":[]},"mechanistic_narrative":"53BP1 is a central chromatin-based scaffold that directs DNA double-strand break repair pathway choice by promoting non-homologous end joining (NHEJ) and suppressing homologous recombination, while also amplifying p53 signaling and safeguarding genome integrity during replication and mitosis. Recruitment to DSBs requires bivalent nucleosome recognition — the tandem Tudor domain binds H4K20me2 while the UDR motif engages RNF168-catalyzed H2AK15ub, as revealed by cryo-EM — and this recognition is gated by regulators including TIRR (which masks the Tudor domain), SPOP-mediated ubiquitination (which extracts 53BP1 from chromatin in S phase), CBP/HDAC2-controlled UDR acetylation, and cell-cycle-dependent H4K20me2 dilution during replication [PMID:27462807, PMID:28241136, PMID:34144977, PMID:29190394, PMID:28564601]. ATM-dependent phosphorylation of 53BP1 recruits distinct effectors — RIF1 via LxL-phosphopeptide motifs and PTIP via separate phospho-sites — with RIF1 in turn recruiting the shieldin complex (SHLD1–SHLD2–SHLD3–REV7) and CST–Polα to protect DNA ends from resection and execute fill-in synthesis, collectively enabling class-switch recombination and long-range V(D)J joining [PMID:23727112, PMID:35216668, PMID:30022168, PMID:30022158, PMID:18931658]. Beyond DSB repair, 53BP1 undergoes liquid–liquid phase separation that concentrates p53 and amplifies its transcriptional output, forms nuclear bodies that restrain replication timing of under-replicated loci, and functions with USP28 and TP53 in a mitotic surveillance pathway that eliminates cells after prolonged mitosis [PMID:31267591, PMID:30804506, PMID:33226141]."},"prefetch_data":{"uniprot":{"accession":"Q12888","full_name":"TP53-binding protein 1","aliases":[],"length_aa":1972,"mass_kda":213.6,"function":"Double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis (PubMed:12364621, PubMed:17190600, PubMed:21144835, PubMed:22553214, PubMed:23333306, PubMed:27153538, PubMed:28241136, PubMed:31135337, PubMed:37696958). Plays a key role in the repair of double-strand DNA breaks (DSBs) in response to DNA damage by promoting non-homologous end joining (NHEJ)-mediated repair of DSBs and specifically counteracting the function of the homologous recombination (HR) repair protein BRCA1 (PubMed:22553214, PubMed:23333306, PubMed:23727112, PubMed:27153538, PubMed:31135337). In response to DSBs, phosphorylation by ATM promotes interaction with RIF1 and dissociation from NUDT16L1/TIRR, leading to recruitment to DSBs sites (PubMed:28241136). Recruited to DSBs sites by recognizing and binding histone H2A monoubiquitinated at 'Lys-15' (H2AK15Ub) and histone H4 dimethylated at 'Lys-20' (H4K20me2), two histone marks that are present at DSBs sites (PubMed:17190600, PubMed:23760478, PubMed:27153538, PubMed:28241136). Required for immunoglobulin class-switch recombination (CSR) during antibody genesis, a process that involves the generation of DNA DSBs (PubMed:23345425). Participates in the repair and the orientation of the broken DNA ends during CSR (By similarity). In contrast, it is not required for classic NHEJ and V(D)J recombination (By similarity). Promotes NHEJ of dysfunctional telomeres via interaction with PAXIP1 (PubMed:23727112)","subcellular_location":"Nucleus; Chromosome; Chromosome, centromere, kinetochore","url":"https://www.uniprot.org/uniprotkb/Q12888/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TP53BP1","classification":"Not Classified","n_dependent_lines":52,"n_total_lines":1208,"dependency_fraction":0.04304635761589404},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DYNLL1","stoichiometry":10.0},{"gene":"DYNLL2","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/TP53BP1","total_profiled":1310},"omim":[{"mim_id":"621534","title":"FAMILY WITH SEQUENCE SIMILARITY 135, MEMBER B; FAM135B","url":"https://www.omim.org/entry/621534"},{"mim_id":"618650","title":"RING FINGER PROTEIN 169; RNF169","url":"https://www.omim.org/entry/618650"},{"mim_id":"618030","title":"SHIELD COMPLEX, SUBUNIT 3; SHLD3","url":"https://www.omim.org/entry/618030"},{"mim_id":"618029","title":"SHIELD COMPLEX, SUBUNIT 2; SHLD2","url":"https://www.omim.org/entry/618029"},{"mim_id":"618028","title":"SHIELD COMPLEX, SUBUNIT 1; SHLD1","url":"https://www.omim.org/entry/618028"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nuclear bodies","reliability":"Enhanced"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TP53BP1"},"hgnc":{"alias_symbol":["53BP1","p202","TDRD30"],"prev_symbol":[]},"alphafold":{"accession":"Q12888","domains":[{"cath_id":"-","chopping":"1239-1270","consensus_level":"high","plddt":84.2325,"start":1239,"end":1270},{"cath_id":"2.30.30.30","chopping":"1490-1601","consensus_level":"medium","plddt":91.8269,"start":1490,"end":1601},{"cath_id":"3.40.50.10190","chopping":"1722-1743_1771-1966","consensus_level":"medium","plddt":93.7705,"start":1722,"end":1966}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q12888","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q12888-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q12888-F1-predicted_aligned_error_v6.png","plddt_mean":43.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TP53BP1","jax_strain_url":"https://www.jax.org/strain/search?query=TP53BP1"},"sequence":{"accession":"Q12888","fasta_url":"https://rest.uniprot.org/uniprotkb/Q12888.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q12888/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q12888"}},"corpus_meta":[{"pmid":"24326623","id":"PMC_24326623","title":"Double-strand break repair: 53BP1 comes into focus.","date":"2013","source":"Nature reviews. Molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/24326623","citation_count":868,"is_preprint":false},{"pmid":"30022168","id":"PMC_30022168","title":"The shieldin complex mediates 53BP1-dependent DNA repair.","date":"2018","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/30022168","citation_count":500,"is_preprint":false},{"pmid":"11331310","id":"PMC_11331310","title":"Tumor suppressor p53 binding protein 1 (53BP1) is involved in DNA damage-signaling pathways.","date":"2001","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/11331310","citation_count":418,"is_preprint":false},{"pmid":"31267591","id":"PMC_31267591","title":"Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments.","date":"2019","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/31267591","citation_count":358,"is_preprint":false},{"pmid":"30022158","id":"PMC_30022158","title":"53BP1-RIF1-shieldin counteracts DSB resection through CST- and Polα-dependent fill-in.","date":"2018","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/30022158","citation_count":350,"is_preprint":false},{"pmid":"21293379","id":"PMC_21293379","title":"MMSET regulates histone H4K20 methylation and 53BP1 accumulation at DNA damage sites.","date":"2011","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/21293379","citation_count":334,"is_preprint":false},{"pmid":"24094932","id":"PMC_24094932","title":"53BP1: pro choice in DNA repair.","date":"2013","source":"Trends in cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/24094932","citation_count":302,"is_preprint":false},{"pmid":"12697768","id":"PMC_12697768","title":"Accumulation of checkpoint protein 53BP1 at DNA breaks involves its binding to phosphorylated histone H2AX.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12697768","citation_count":301,"is_preprint":false},{"pmid":"11238909","id":"PMC_11238909","title":"Phosphorylation and rapid relocalization of 53BP1 to nuclear foci upon DNA damage.","date":"2001","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11238909","citation_count":300,"is_preprint":false},{"pmid":"23727112","id":"PMC_23727112","title":"53BP1 mediates productive and mutagenic DNA repair through distinct phosphoprotein interactions.","date":"2013","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/23727112","citation_count":292,"is_preprint":false},{"pmid":"18931658","id":"PMC_18931658","title":"53BP1 facilitates long-range DNA end-joining during V(D)J recombination.","date":"2008","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/18931658","citation_count":260,"is_preprint":false},{"pmid":"30046110","id":"PMC_30046110","title":"53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ.","date":"2018","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/30046110","citation_count":252,"is_preprint":false},{"pmid":"27462807","id":"PMC_27462807","title":"The structural basis of modified nucleosome recognition by 53BP1.","date":"2016","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/27462807","citation_count":201,"is_preprint":false},{"pmid":"21549309","id":"PMC_21549309","title":"Regulation of DNA end joining, resection, and immunoglobulin class switch recombination by 53BP1.","date":"2011","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/21549309","citation_count":198,"is_preprint":false},{"pmid":"29176614","id":"PMC_29176614","title":"Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency.","date":"2017","source":"Nature biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/29176614","citation_count":197,"is_preprint":false},{"pmid":"27348077","id":"PMC_27348077","title":"53BP1 fosters fidelity of homology-directed DNA repair.","date":"2016","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/27348077","citation_count":185,"is_preprint":false},{"pmid":"31896689","id":"PMC_31896689","title":"53BP1: a DSB escort.","date":"2020","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/31896689","citation_count":175,"is_preprint":false},{"pmid":"8524315","id":"PMC_8524315","title":"The interferon-inducible p202 protein as a modulator of transcription: inhibition of NF-kappa B, c-Fos, and c-Jun activities.","date":"1996","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8524315","citation_count":142,"is_preprint":false},{"pmid":"17575156","id":"PMC_17575156","title":"Cytoplasmic irradiation induces mitochondrial-dependent 53BP1 protein relocalization in irradiated and bystander cells.","date":"2007","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/17575156","citation_count":133,"is_preprint":false},{"pmid":"23329852","id":"PMC_23329852","title":"Histone H4 deacetylation facilitates 53BP1 DNA damage signaling and double-strand break repair.","date":"2013","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/23329852","citation_count":128,"is_preprint":false},{"pmid":"24320053","id":"PMC_24320053","title":"Role of 53BP1 in the regulation of DNA double-strand break repair pathway choice.","date":"2013","source":"Radiation research","url":"https://pubmed.ncbi.nlm.nih.gov/24320053","citation_count":121,"is_preprint":false},{"pmid":"28241136","id":"PMC_28241136","title":"TIRR regulates 53BP1 by masking its histone methyl-lysine binding function.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28241136","citation_count":110,"is_preprint":false},{"pmid":"7890747","id":"PMC_7890747","title":"Binding of an interferon-inducible protein (p202) to the retinoblastoma protein.","date":"1995","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7890747","citation_count":105,"is_preprint":false},{"pmid":"30497961","id":"PMC_30497961","title":"53BP1: A key player of DNA damage response with critical functions in cancer.","date":"2018","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/30497961","citation_count":105,"is_preprint":false},{"pmid":"28564601","id":"PMC_28564601","title":"Replication-Coupled Dilution of H4K20me2 Guides 53BP1 to Pre-replicative Chromatin.","date":"2017","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/28564601","citation_count":103,"is_preprint":false},{"pmid":"31653568","id":"PMC_31653568","title":"53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination.","date":"2019","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/31653568","citation_count":100,"is_preprint":false},{"pmid":"8896460","id":"PMC_8896460","title":"Inhibition of E2F-mediated transcription by p202.","date":"1996","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/8896460","citation_count":95,"is_preprint":false},{"pmid":"36894671","id":"PMC_36894671","title":"SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence.","date":"2023","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/36894671","citation_count":94,"is_preprint":false},{"pmid":"26344695","id":"PMC_26344695","title":"Chemical proteomics reveals a γH2AX-53BP1 interaction in the DNA damage response.","date":"2015","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/26344695","citation_count":93,"is_preprint":false},{"pmid":"30559443","id":"PMC_30559443","title":"The ASCIZ-DYNLL1 axis promotes 53BP1-dependent non-homologous end joining and PARP inhibitor sensitivity.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30559443","citation_count":87,"is_preprint":false},{"pmid":"30804506","id":"PMC_30804506","title":"53BP1 nuclear bodies enforce replication timing at under-replicated DNA to limit heritable DNA damage.","date":"2019","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/30804506","citation_count":86,"is_preprint":false},{"pmid":"35042897","id":"PMC_35042897","title":"53BP1 regulates heterochromatin through liquid phase separation.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/35042897","citation_count":85,"is_preprint":false},{"pmid":"33087281","id":"PMC_33087281","title":"Roles for 53BP1 in the repair of radiation-induced DNA double strand breaks.","date":"2020","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/33087281","citation_count":85,"is_preprint":false},{"pmid":"24324146","id":"PMC_24324146","title":"RNF168 ubiquitylates 53BP1 and controls its response to DNA double-strand breaks.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/24324146","citation_count":85,"is_preprint":false},{"pmid":"21278454","id":"PMC_21278454","title":"BRCA1, PARP, and 53BP1: conditional synthetic lethality and synthetic viability.","date":"2011","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/21278454","citation_count":84,"is_preprint":false},{"pmid":"16024119","id":"PMC_16024119","title":"ATM signaling and 53BP1.","date":"2005","source":"Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/16024119","citation_count":81,"is_preprint":false},{"pmid":"24953651","id":"PMC_24953651","title":"MOF phosphorylation by ATM regulates 53BP1-mediated double-strand break repair pathway choice.","date":"2014","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/24953651","citation_count":81,"is_preprint":false},{"pmid":"34555355","id":"PMC_34555355","title":"Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps.","date":"2021","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/34555355","citation_count":77,"is_preprint":false},{"pmid":"28506460","id":"PMC_28506460","title":"Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/28506460","citation_count":76,"is_preprint":false},{"pmid":"20871591","id":"PMC_20871591","title":"TopBP1 functions with 53BP1 in the G1 DNA damage checkpoint.","date":"2010","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/20871591","citation_count":76,"is_preprint":false},{"pmid":"23850291","id":"PMC_23850291","title":"Molecular mechanism for p202-mediated specific inhibition of AIM2 inflammasome activation.","date":"2013","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/23850291","citation_count":74,"is_preprint":false},{"pmid":"30257212","id":"PMC_30257212","title":"BRCA1 Mutation-Specific Responses to 53BP1 Loss-Induced Homologous Recombination and PARP Inhibitor Resistance.","date":"2018","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/30257212","citation_count":70,"is_preprint":false},{"pmid":"16492765","id":"PMC_16492765","title":"53BP1 and p53 synergize to suppress genomic instability and lymphomagenesis.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/16492765","citation_count":66,"is_preprint":false},{"pmid":"29106372","id":"PMC_29106372","title":"53BP1 and BRCA1 control pathway choice for stalled replication restart.","date":"2017","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/29106372","citation_count":65,"is_preprint":false},{"pmid":"33961796","id":"PMC_33961796","title":"AHNAK controls 53BP1-mediated p53 response by restraining 53BP1 oligomerization and phase separation.","date":"2021","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/33961796","citation_count":65,"is_preprint":false},{"pmid":"9233764","id":"PMC_9233764","title":"Inhibition of E2F-4/DP-1-stimulated transcription by p202.","date":"1997","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/9233764","citation_count":65,"is_preprint":false},{"pmid":"11013253","id":"PMC_11013253","title":"The gene encoding p202, an interferon-inducible negative regulator of the p53 tumor suppressor, is a target of p53-mediated transcriptional repression.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11013253","citation_count":64,"is_preprint":false},{"pmid":"27462418","id":"PMC_27462418","title":"Cell cycle-dependent inhibition of 53BP1 signaling by BRCA1.","date":"2015","source":"Cell discovery","url":"https://pubmed.ncbi.nlm.nih.gov/27462418","citation_count":62,"is_preprint":false},{"pmid":"29378830","id":"PMC_29378830","title":"53BP1 Mediates ATR-Chk1 Signaling and Protects Replication Forks under Conditions of Replication Stress.","date":"2018","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29378830","citation_count":61,"is_preprint":false},{"pmid":"34606602","id":"PMC_34606602","title":"Oncogenic KRAS drives radioresistance through upregulation of NRF2-53BP1-mediated non-homologous end-joining repair.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34606602","citation_count":57,"is_preprint":false},{"pmid":"32759981","id":"PMC_32759981","title":"PRMT5 promotes DNA repair through methylation of 53BP1 and is regulated by Src-mediated phosphorylation.","date":"2020","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/32759981","citation_count":56,"is_preprint":false},{"pmid":"33226141","id":"PMC_33226141","title":"Centrosome defects cause microcephaly by activating the 53BP1-USP28-TP53 mitotic surveillance pathway.","date":"2020","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/33226141","citation_count":53,"is_preprint":false},{"pmid":"11991834","id":"PMC_11991834","title":"Interferon-inducible p202 in the susceptibility to systemic lupus.","date":"2002","source":"Frontiers in bioscience : a journal and virtual library","url":"https://pubmed.ncbi.nlm.nih.gov/11991834","citation_count":52,"is_preprint":false},{"pmid":"29651020","id":"PMC_29651020","title":"GFI1 facilitates efficient DNA repair by regulating PRMT1 dependent methylation of MRE11 and 53BP1.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29651020","citation_count":52,"is_preprint":false},{"pmid":"18986980","id":"PMC_18986980","title":"The direct interaction between 53BP1 and MDC1 is required for the recruitment of 53BP1 to sites of damage.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18986980","citation_count":51,"is_preprint":false},{"pmid":"30602538","id":"PMC_30602538","title":"Mitotic regulators TPX2 and Aurora A protect DNA forks during replication stress by counteracting 53BP1 function.","date":"2019","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/30602538","citation_count":49,"is_preprint":false},{"pmid":"29190394","id":"PMC_29190394","title":"Acetylation of 53BP1 dictates the DNA double strand break repair pathway.","date":"2018","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/29190394","citation_count":48,"is_preprint":false},{"pmid":"38244928","id":"PMC_38244928","title":"Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer.","date":"2024","source":"Annals of oncology : official journal of the European Society for Medical Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38244928","citation_count":47,"is_preprint":false},{"pmid":"28803425","id":"PMC_28803425","title":"Frameshift Mutations in Repeat Sequences of ANK3, HACD4, TCP10L, TP53BP1, MFN1, LCMT2, RNMT, TRMT6, METTL8 and METTL16 Genes in Colon Cancers.","date":"2017","source":"Pathology oncology research : POR","url":"https://pubmed.ncbi.nlm.nih.gov/28803425","citation_count":47,"is_preprint":false},{"pmid":"34144977","id":"PMC_34144977","title":"ATM-phosphorylated SPOP contributes to 53BP1 exclusion from chromatin during DNA replication.","date":"2021","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/34144977","citation_count":47,"is_preprint":false},{"pmid":"31135337","id":"PMC_31135337","title":"Phosphorylation-mediated interactions with TOPBP1 couple 53BP1 and 9-1-1 to control the G1 DNA damage checkpoint.","date":"2019","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/31135337","citation_count":46,"is_preprint":false},{"pmid":"35583003","id":"PMC_35583003","title":"Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review).","date":"2022","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35583003","citation_count":45,"is_preprint":false},{"pmid":"30104380","id":"PMC_30104380","title":"RNF169 limits 53BP1 deposition at DSBs to stimulate single-strand annealing repair.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30104380","citation_count":45,"is_preprint":false},{"pmid":"29844495","id":"PMC_29844495","title":"Structural basis for recognition of 53BP1 tandem Tudor domain by TIRR.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29844495","citation_count":44,"is_preprint":false},{"pmid":"22421153","id":"PMC_22421153","title":"Discordance between phosphorylation and recruitment of 53BP1 in response to DNA double-strand breaks.","date":"2012","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/22421153","citation_count":42,"is_preprint":false},{"pmid":"19414588","id":"PMC_19414588","title":"PTIP regulates 53BP1 and SMC1 at the DNA damage sites.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19414588","citation_count":41,"is_preprint":false},{"pmid":"34452908","id":"PMC_34452908","title":"Lamin B1 sequesters 53BP1 to control its recruitment to DNA damage.","date":"2021","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/34452908","citation_count":41,"is_preprint":false},{"pmid":"29445165","id":"PMC_29445165","title":"53BP1 can limit sister-chromatid rupture and rearrangements driven by a distinct ultrafine DNA bridging-breakage process.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29445165","citation_count":41,"is_preprint":false},{"pmid":"29160738","id":"PMC_29160738","title":"H4K20me2 distinguishes pre-replicative from post-replicative chromatin to appropriately direct DNA repair pathway choice by 53BP1-RIF1-MAD2L2.","date":"2018","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/29160738","citation_count":41,"is_preprint":false},{"pmid":"25422456","id":"PMC_25422456","title":"UbcH7 regulates 53BP1 stability and DSB repair.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25422456","citation_count":40,"is_preprint":false},{"pmid":"25049398","id":"PMC_25049398","title":"Lysine methylation-dependent binding of 53BP1 to the pRb tumor suppressor.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25049398","citation_count":40,"is_preprint":false},{"pmid":"30982887","id":"PMC_30982887","title":"LC8/DYNLL1 is a 53BP1 effector and regulates checkpoint activation.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/30982887","citation_count":39,"is_preprint":false},{"pmid":"18337245","id":"PMC_18337245","title":"RNF8-dependent and RNF8-independent regulation of 53BP1 in response to DNA damage.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18337245","citation_count":39,"is_preprint":false},{"pmid":"35017534","id":"PMC_35017534","title":"BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/35017534","citation_count":38,"is_preprint":false},{"pmid":"33188174","id":"PMC_33188174","title":"Spatiotemporal dynamics of 53BP1 dimer recruitment to a DNA double strand break.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33188174","citation_count":37,"is_preprint":false},{"pmid":"33730584","id":"PMC_33730584","title":"DSB repair pathway choice is regulated by recruitment of 53BP1 through cell cycle-dependent regulation of Sp1.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/33730584","citation_count":37,"is_preprint":false},{"pmid":"9989832","id":"PMC_9989832","title":"Reduced growth rate and transformation phenotype of the prostate cancer cells by an interferon-inducible protein, p202.","date":"1999","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/9989832","citation_count":36,"is_preprint":false},{"pmid":"33188175","id":"PMC_33188175","title":"CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33188175","citation_count":36,"is_preprint":false},{"pmid":"10646849","id":"PMC_10646849","title":"Tumor suppression and sensitization to tumor necrosis factor alpha-induced apoptosis by an interferon-inducible protein, p202, in breast cancer cells.","date":"2000","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/10646849","citation_count":35,"is_preprint":false},{"pmid":"35216668","id":"PMC_35216668","title":"RIF1 acts in DNA repair through phosphopeptide recognition of 53BP1.","date":"2022","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/35216668","citation_count":34,"is_preprint":false},{"pmid":"31911551","id":"PMC_31911551","title":"Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation.","date":"2020","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/31911551","citation_count":33,"is_preprint":false},{"pmid":"30312172","id":"PMC_30312172","title":"H3K9me3 and H4K20me3 represent the epigenetic landscape for 53BP1 binding to DNA lesions.","date":"2018","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/30312172","citation_count":33,"is_preprint":false},{"pmid":"36553657","id":"PMC_36553657","title":"53BP1: Keeping It under Control, Even at a Distance from DNA Damage.","date":"2022","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/36553657","citation_count":32,"is_preprint":false},{"pmid":"11585747","id":"PMC_11585747","title":"p202, an interferon-inducible protein, mediates multiple antitumor activities in human pancreatic cancer xenograft models.","date":"2001","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/11585747","citation_count":32,"is_preprint":false},{"pmid":"36642815","id":"PMC_36642815","title":"DNA damage-induced cellular senescence is regulated by 53BP1 accumulation in the nuclear foci and phase separation.","date":"2023","source":"Cell proliferation","url":"https://pubmed.ncbi.nlm.nih.gov/36642815","citation_count":32,"is_preprint":false},{"pmid":"33596428","id":"PMC_33596428","title":"AMPK-mediated phosphorylation on 53BP1 promotes c-NHEJ.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/33596428","citation_count":30,"is_preprint":false},{"pmid":"19176521","id":"PMC_19176521","title":"Protein phosphatase 5 regulates the function of 53BP1 after neocarzinostatin-induced DNA damage.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19176521","citation_count":30,"is_preprint":false},{"pmid":"30812030","id":"PMC_30812030","title":"The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/30812030","citation_count":30,"is_preprint":false},{"pmid":"29206178","id":"PMC_29206178","title":"Around and beyond 53BP1 Nuclear Bodies.","date":"2017","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/29206178","citation_count":28,"is_preprint":false},{"pmid":"10074903","id":"PMC_10074903","title":"Retardation of cell proliferation after expression of p202 accompanies an increase in p21(WAF1/CIP1).","date":"1999","source":"Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/10074903","citation_count":28,"is_preprint":false},{"pmid":"33961797","id":"PMC_33961797","title":"TIRR inhibits the 53BP1-p53 complex to alter cell-fate programs.","date":"2021","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/33961797","citation_count":28,"is_preprint":false},{"pmid":"28969073","id":"PMC_28969073","title":"γH2AX, 53BP1 and Rad51 protein foci changes in mesenchymal stem cells during prolonged X-ray irradiation.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/28969073","citation_count":28,"is_preprint":false},{"pmid":"28958991","id":"PMC_28958991","title":"Pathway-Enriched Gene Signature Associated with 53BP1 Response to PARP Inhibition in Triple-Negative Breast Cancer.","date":"2017","source":"Molecular cancer therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/28958991","citation_count":27,"is_preprint":false},{"pmid":"36136101","id":"PMC_36136101","title":"Individual radiosensitivity reflected by γ-H2AX and 53BP1 foci predicts outcome in PSMA-targeted radioligand therapy.","date":"2022","source":"European journal of nuclear medicine and molecular imaging","url":"https://pubmed.ncbi.nlm.nih.gov/36136101","citation_count":27,"is_preprint":false},{"pmid":"32576832","id":"PMC_32576832","title":"Rad9/53BP1 promotes DNA repair via crossover recombination by limiting the Sgs1 and Mph1 helicases.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32576832","citation_count":26,"is_preprint":false},{"pmid":"11687962","id":"PMC_11687962","title":"p202, an interferon-inducible negative regulator of cell growth, is a target of the adenovirus E1A protein.","date":"2001","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/11687962","citation_count":25,"is_preprint":false},{"pmid":"37377435","id":"PMC_37377435","title":"ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex.","date":"2023","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/37377435","citation_count":25,"is_preprint":false},{"pmid":"26615718","id":"PMC_26615718","title":"Functional crosstalk between DNA damage response proteins 53BP1 and BRCA1 regulates double strand break repair choice.","date":"2015","source":"Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/26615718","citation_count":25,"is_preprint":false},{"pmid":"25916843","id":"PMC_25916843","title":"Ectopic expression of RNF168 and 53BP1 increases mutagenic but not physiological non-homologous end joining.","date":"2015","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/25916843","citation_count":24,"is_preprint":false},{"pmid":"27573809","id":"PMC_27573809","title":"DNA Damage Detection by 53BP1: Relationship to Species Longevity.","date":"2017","source":"The journals of gerontology. Series A, Biological sciences and medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/27573809","citation_count":24,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":43798,"output_tokens":11725,"usd":0.153635},"stage2":{"model":"claude-opus-4-6","input_tokens":15846,"output_tokens":4288,"usd":0.279645},"total_usd":0.43328,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"53BP1 becomes hyperphosphorylated and forms discrete nuclear foci in response to DNA damage; ATM-deficient cells show no 53BP1 hyperphosphorylation and reduced foci formation; 53BP1 is phosphorylated by ATM in vitro, establishing 53BP1 as an ATM substrate in DNA damage signaling.\",\n      \"method\": \"Immunofluorescence, in vitro kinase assay, ATM-deficient cell lines, wortmannin inhibition\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro kinase assay plus genetic (ATM-deficient cells) and pharmacological validation, replicated across labs\",\n      \"pmids\": [\"11331310\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"53BP1 localizes to chromatin and forms nuclear foci upon DNA damage; Xenopus 53BP1 is hyperphosphorylated after X-ray irradiation in an ATM kinase-dependent manner; inhibitors of ATM-related kinases delay relocalization and reduce phosphorylation of 53BP1.\",\n      \"method\": \"Live cell imaging, immunofluorescence, X-irradiation, ATM kinase inhibitors, AT cells\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic and pharmacological evidence in Xenopus and human AT cells, consistent with PMID:11331310\",\n      \"pmids\": [\"11238909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"A region upstream of the 53BP1 C-terminus is required and sufficient for recruitment to DNA break sites by directly binding phosphorylated H2AX (γH2AX) but not unphosphorylated H2AX; H2AX phosphorylation at serine 140 is critical for 53BP1 foci formation; ATM-mediated N-terminal phosphorylation of 53BP1 is not required for its relocalization.\",\n      \"method\": \"In vitro binding assay, H2AX-deficient cell reconstitution with wild-type or phospho-deficient H2AX, domain mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro binding assay plus genetic reconstitution with phospho-deficient mutant\",\n      \"pmids\": [\"12697768\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"53BP1 facilitates long-range DNA end-joining during V(D)J recombination; 53BP1-deficient lymphocytes show impaired distal V-DJ joining with extensive degradation of unrepaired coding ends, demonstrating a role in genomic stability during long-range joining of DNA breaks distinct from classical NHEJ.\",\n      \"method\": \"53BP1 knockout mouse model, V(D)J recombination assay, genomic analysis of TCR locus\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular and molecular phenotype\",\n      \"pmids\": [\"18931658\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"53BP1 and MDC1 interact directly through the tandem BRCT domain of MDC1 and residues 1288–1409 of 53BP1; this interaction is required for recruitment of 53BP1 to DSB sites; after DSB induction, the interaction is reduced due to competition between γH2AX and 53BP1 for MDC1 BRCT domain binding; the interaction is enhanced during mitosis in a phospho-dependent manner.\",\n      \"method\": \"Co-IP, pulldown, domain mapping, immunofluorescence in H2AX-deficient and MDC1-deficient cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with domain mapping and functional validation in relevant cell lines\",\n      \"pmids\": [\"18986980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"PTIP regulates 53BP1 localization to DNA damage sites downstream of RNF8; PTIP depletion prevents 53BP1 foci formation; SMC1 phosphorylation at DSB sites is dependent on PTIP, placing PTIP between RNF8 and 53BP1 in the DNA damage signaling pathway.\",\n      \"method\": \"siRNA knockdown, co-IP, immunofluorescence, epistasis analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis by siRNA with defined pathway placement; single lab\",\n      \"pmids\": [\"19414588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Protein phosphatase 5 (PP5) binds 53BP1 and dephosphorylates it at Ser-25 and Ser-1778 after DNA damage; PP5 overexpression accelerates 53BP1 dephosphorylation and reduces phospho-53BP1 foci; PP5 downregulation inhibits dephosphorylation, prolonging foci; PP5 overexpression reduces NHEJ activity.\",\n      \"method\": \"Yeast two-hybrid, co-IP, overexpression/knockdown in U2OS cells, NHEJ reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — yeast two-hybrid plus co-IP and functional assay; single lab\",\n      \"pmids\": [\"19176521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"TopBP1 colocalizes with 53BP1 at DSBs in G1 phase; TopBP1 BRCT domains 4-5 interact with 53BP1; recruitment of TopBP1 to DSBs in G1 is dependent on 53BP1; loss of TopBP1 or 53BP1 causes G1 DNA damage checkpoint defects.\",\n      \"method\": \"Co-IP, siRNA knockdown, immunofluorescence, G1 checkpoint assay (S-phase entry after irradiation)\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal interaction plus epistatic checkpoint phenotype\",\n      \"pmids\": [\"20871591\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"53BP1 facilitates joining of intrachromosomal DSBs only at distances corresponding to γH2AX spreading (~1 Mb); DNA end protection by 53BP1 is distance-independent; chromatin association, oligomerization, and N-terminal ATM phosphorylation of 53BP1 are all required for DNA end protection and CSR.\",\n      \"method\": \"Paired DSB joining assay across chromosomal distances, 53BP1 mutant analysis, class switch recombination assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple 53BP1 structural mutants tested with quantitative joining and CSR assays\",\n      \"pmids\": [\"21549309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"MMSET (NSD2/WHSC1) is recruited to DSBs via the γH2AX-MDC1 pathway (MDC1 BRCT domain binds phospho-Ser102 of MMSET) and locally methylates H4K20 at DSBs; this local increase in H4K20me2 is required for 53BP1 recruitment; MMSET knockdown significantly decreases H4K20me2 at DSBs and subsequent 53BP1 accumulation.\",\n      \"method\": \"ChIP, siRNA knockdown, co-IP, immunofluorescence, H4K20 methylation assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (ChIP, co-IP, KD) in a single study with clear mechanistic pathway\",\n      \"pmids\": [\"21293379\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"53BP1 promotes productive CSR and suppresses mutagenic DNA repair through distinct phosphodependent interactions: ATM-mediated phosphorylation of S/TQ sites recruits RIF1 (via 8 N-terminal sites) for end-blocking, while separate phosphorylation recruits PTIP for CSR; a 53BP1-8A phosphomutant recruits RIF1 but not PTIP.\",\n      \"method\": \"53BP1 phosphomutant knock-in mice, CSR assay, immunofluorescence, co-IP\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — phosphomutant knock-in with multiple functional readouts (CSR, NHEJ, HR) and interactor recruitment\",\n      \"pmids\": [\"23727112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"53BP1 phase separates to form liquid-like repair compartments at DSBs; 53BP1 assembly is sensitive to osmotic pressure, temperature, salt, and hydrophobic interactions; p53 is enriched within 53BP1 optoDroplets; disruption of 53BP1 phase separation impairs p53 induction and p53 target gene expression.\",\n      \"method\": \"Live cell microscopy, CRISPR endogenous tagging, optoDroplet experiments, osmotic/chemical perturbations\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including optoDroplet, live imaging, and functional p53 readout\",\n      \"pmids\": [\"31267591\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RNF168 mediates K63-linked ubiquitylation of 53BP1, which is required for initial recruitment of 53BP1 to DSBs and for its function in DNA repair, checkpoint activation, and genomic integrity.\",\n      \"method\": \"Ubiquitylation assay, co-IP, RNF168 KO/KD cells, immunofluorescence\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — biochemical ubiquitylation assay plus functional validation in KO cells\",\n      \"pmids\": [\"24324146\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"H4K16 acetylation antagonizes 53BP1 binding to H4K20me2; DNA damage induces transient, localized H4 deacetylation at DSBs which facilitates 53BP1 foci formation and NHEJ; 53BP1 foci assemble primarily on H4K20me2 established by SETD8 and SUV420 methyltransferases, not de novo MMSET-mediated methylation.\",\n      \"method\": \"Chromatin fractionation, siRNA knockdown of methyltransferases/HDAC, NHEJ reporter, immunofluorescence\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple knockdowns with functional assay; single lab\",\n      \"pmids\": [\"23329852\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"53BP1 tandem Tudor domain binds methylated K810 of pRb; structural elucidation reveals recognition of the methylated lysine and surrounding residues; 53BP1 binding to methyl-K810 pRb occurs at E2F target genes, integrating pRb activity with the DNA damage response.\",\n      \"method\": \"Structural biology (crystal structure), binding assay, ChIP\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus functional ChIP validation\",\n      \"pmids\": [\"25049398\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"UbcH7 (Ube2L3) regulates steady-state and replication stress-induced ubiquitination and proteasome-dependent degradation of 53BP1; N-terminal phosphorylation of 53BP1 is involved in replication stress-induced degradation; UbcH7 depletion stabilizes 53BP1, inhibits DSB end resection, increases NHEJ and decreases HR.\",\n      \"method\": \"shRNA screen, ubiquitination assay, NHEJ/HR reporter, immunoprecipitation\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — shRNA screen plus biochemical and functional validation; single lab\",\n      \"pmids\": [\"25422456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ATM-dependent MOF phosphorylation at T392 colocalizes with 53BP1 at DSBs; MOF-T392A mutation blocks reduction of DSB-associated 53BP1 in S/G2 phase, enhances 53BP1 and reduces BRCA1 at DSBs, and impairs HR repair.\",\n      \"method\": \"Phospho-mutant expression, immunofluorescence, co-IP, HR reporter assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — phosphomutant with HR assay and localization data; single lab\",\n      \"pmids\": [\"24953651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Chemical proteomics identified 53BP1 as a direct γH2AX binder through its BRCT domains; a 53BP1 mutant deficient in γH2AX binding shows altered localization to chromosomal breaks, revealing that direct γH2AX recognition by the BRCT domains modulates 53BP1 localization at damage sites.\",\n      \"method\": \"Quantitative chemical proteomics (γH2AX affinity pulldown from native proteome), mutant localization assay\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — native proteome pulldown plus mutagenesis with functional localization readout\",\n      \"pmids\": [\"26344695\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"BRCA1 inhibits ATM-dependent 53BP1 phosphorylation in S/G2 phases, restricting RIF1 and PTIP accumulation at DSBs to G1; both BRCT and RING domains of BRCA1 are required for inhibition of 53BP1 phosphorylation, ensuring HR predominates in S/G2.\",\n      \"method\": \"Cell cycle-sorted cells, phospho-specific antibodies, immunofluorescence, BRCA1 domain mutants\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — domain mutant analysis with cell cycle-specific phosphorylation readout; single lab\",\n      \"pmids\": [\"27462418\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Cryo-EM structure of dimerized human 53BP1 bound to H4K20me2- and H2AK15ub-containing nucleosome (NCP-ubme) at 4.5 Å; reveals simultaneous engagement of H4K20me2 by tandem Tudor domain and H2AK15ub by UDR motif; ubiquitin is sandwiched between UDR and NCP surface; two arginine fingers in H2A tail position ubiquitin and confer selectivity for H2AK15ub over H2AK13ub; intimate contacts with the nucleosomal acidic patch are required.\",\n      \"method\": \"Cryo-EM structure determination at 4.5 Å, biochemical validation\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with mechanistic detail of dual histone mark recognition\",\n      \"pmids\": [\"27462807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Silencing 53BP1 or exhausting its chromatin-binding capacity switches DSB repair from error-free gene conversion (RAD51) to mutagenic single-strand annealing (RAD52), demonstrating that 53BP1 fosters fidelity of HDR rather than simply suppressing it.\",\n      \"method\": \"siRNA knockdown, HR sub-pathway reporter assays, RAD51/RAD52 focus formation\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple HR sub-pathway reporters plus focus formation; single lab\",\n      \"pmids\": [\"27348077\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TIRR directly binds the tandem Tudor domain of 53BP1 and masks its H4K20me2 binding motif, preventing 53BP1 recruitment to DSBs; ATM phosphorylation of 53BP1 after DNA damage recruits RIF1 and dissociates the 53BP1-TIRR complex; TIRR overexpression impedes 53BP1 function; TIRR depletion destabilizes soluble 53BP1.\",\n      \"method\": \"Co-IP, pulldown, immunofluorescence, ATM inhibition, Tudor domain binding competition assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP, competition binding, multiple functional readouts; single lab with comprehensive validation\",\n      \"pmids\": [\"28241136\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structure of TIRR in complex with 53BP1 tandem Tudor domain at 1.76 Å; N-terminal region (residues 10-24) and L8-loop of TIRR interact with 53BP1 Tudor through loops L1, L3, and L1'; TIRR histidine H106 is essential for 53BP1 Tudor binding; TIRR recognition blocks H4K20me2 binding.\",\n      \"method\": \"X-ray crystallography, NMR, mutagenesis, in vivo functional assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — atomic resolution crystal structure with mutagenesis and functional validation\",\n      \"pmids\": [\"29844495\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NMR and biochemistry reveal that RNF169 bridges ubiquitin and histone surfaces on NCP-ubme with high affinity (conformational selection), displacing low-affinity 53BP1 from H2AK15ub nucleosomes; RAD18 also binds NCP-ubme through a ubiquitin-binding domain that contacts sites accessed by 53BP1, providing an alternative mechanism for 53BP1 displacement.\",\n      \"method\": \"NMR spectroscopy, biochemical binding assay, competition assays with reconstituted nucleosomes\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — NMR plus reconstitution assays with mechanistic detail\",\n      \"pmids\": [\"28506460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"53BP1 accumulation at DSBs declines as cells progress through S phase due to replication-coupled dilution of H4K20me2; premature maturation of post-replicative chromatin restores H4K20me2 and rescues 53BP1 accumulation, establishing that H4K20me2 availability controls 53BP1-mediated repair pathway choice across the cell cycle.\",\n      \"method\": \"Live cell imaging, cell cycle synchronization, H4K20me2 ChIP, EdU labeling\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and live imaging with mechanistic rescue experiment\",\n      \"pmids\": [\"28564601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"An engineered ubiquitin variant (i53) blocks 53BP1 accumulation at DSBs by inhibiting its UDR/Tudor-mediated chromatin recruitment, increasing HDR-dependent genome editing by up to 5.6-fold, confirming that 53BP1 suppresses end resection as a key step in HDR.\",\n      \"method\": \"Ubiquitin variant library screen, CRISPR-Cas9 HDR assay, immunofluorescence\",\n      \"journal\": \"Nature biotechnology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — biochemical screen plus functional HDR assay; mechanistic inhibitor study\",\n      \"pmids\": [\"29176614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Shieldin complex (SHLD1/C20orf196, SHLD2/FAM35A, SHLD3/CTC-534A2.2, REV7) is a 53BP1 effector that localizes to DSBs in a 53BP1- and RIF1-dependent manner; SHLD2 binds single-stranded DNA via OB-fold domains; loss of shieldin impairs NHEJ, immunoglobulin class switching, causes hyper-resection, and confers PARP inhibitor resistance in BRCA1-deficient cells.\",\n      \"method\": \"Proteomics/MS, co-IP, genetic KO, immunofluorescence, ssDNA binding assay, CSR assay, PARPi sensitivity\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — complex identified by MS, validated by co-IP and KO, with multiple functional assays; replicated in concurrent studies\",\n      \"pmids\": [\"30022168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CST (CTC1-STN1-TEN1) interacts with shieldin downstream of 53BP1-RIF1; CST and Polα localize to DNA damage sites in a 53BP1- and shieldin-dependent manner; CST-Polα-mediated fill-in controls DSB repair by limiting resection; CST depletion increases resection and, in BRCA1-deficient cells, blocks RAD51 loading and diminishes PARPi efficacy.\",\n      \"method\": \"Co-IP, immunofluorescence, siRNA knockdown, resection assays, RAD51 focus formation, PARPi sensitivity\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP plus multiple functional assays; mechanistic fill-in model tested with Polα inhibition\",\n      \"pmids\": [\"30022158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"53BP1 cooperates with REV7 to promote NHEJ during CSR, while REV7 is dispensable for 53BP1-dependent V(D)J recombination; shieldin (REV7-SHLD1-SHLD2-SHLD3) explains this DNA structure specificity by mediating end-protection in ssDNA compartments and is essential for REV7-dependent NHEJ in CSR but dispensable for REV7-dependent interstrand crosslink repair.\",\n      \"method\": \"Mouse genetics (conditional KO), CSR assay, V(D)J recombination analysis, shieldin identification by proteomics\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple KO mouse models plus proteomics identification; independent replication by concurrent shieldin papers\",\n      \"pmids\": [\"30046110\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DYNLL1 directly binds 53BP1 and stimulates 53BP1 oligomerization, promoting 53BP1 recruitment and interaction with DSB-associated chromatin; loss of DYNLL1 or its transcriptional regulator ASCIZ impairs CSR and renders BRCA1-mutant tumors resistant to PARP inhibitors.\",\n      \"method\": \"Co-IP, pulldown, immunofluorescence, DYNLL1 KO mice, CSR assay, PARPi sensitivity assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — co-IP plus multiple functional assays in KO cells/mice\",\n      \"pmids\": [\"30559443\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CBP-mediated acetylation of 53BP1 at K1626/K1628 in the UDR motif disrupts interaction between 53BP1 and nucleosomes, blocking recruitment of 53BP1, PTIP, and RIF1 to DSBs and shifting repair toward HR; HDAC2 reverses this acetylation to maintain NHEJ/HR balance.\",\n      \"method\": \"Co-IP, immunofluorescence, acetylation assay, NHEJ/HR reporter, HDAC2 knockdown\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — biochemical acetylation assay plus functional reporters; single lab\",\n      \"pmids\": [\"29190394\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"GFI1 interacts with PRMT1 and enables PRMT1 to bind and methylate 53BP1 (and MRE11), which is necessary for 53BP1 function in the DNA damage response; GFI1 deletion causes hypersensitivity to ionizing radiation and DNA repair defects.\",\n      \"method\": \"Co-IP, methylation assay, GFI1 KO, immunofluorescence, clonogenic survival\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — co-IP plus methylation assay and KO phenotype; single lab\",\n      \"pmids\": [\"29651020\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"53BP1 enforces two distinct anti-HR blocks: (1) a pre-resection block via PTIP interaction (S25 phosphorylation site) controlling DNA2-dependent end resection, and (2) a post-resection block via shieldin that inhibits RNF168-mediated PALB2/RAD51 loading onto ssDNA.\",\n      \"method\": \"53BP1-S25A knock-in mice crossed with BRCA1Δ11 mice, RAD51/PALB2 focus formation, PARPi sensitivity, epistasis analysis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — knock-in mice with multiple orthogonal mechanistic readouts and epistasis\",\n      \"pmids\": [\"31653568\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"53BP1 nuclear bodies (53BP1-NBs) in G1 daughter cells restrain replication of embedded under-replicated DNA loci until late S phase, enabling RAD52-mediated repair; absence or malfunction of 53BP1-NBs causes premature replication of affected loci and genotoxic RAD51-mediated recombination.\",\n      \"method\": \"Live cell imaging, CRISPR labeling, EdU incorporation, RAD52/RAD51 focus assay, replication timing analysis\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — live imaging plus genetic manipulation with specific replication timing and repair pathway readouts\",\n      \"pmids\": [\"30804506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TOPBP1 BRCT domains selectively bind conserved phosphorylation sites in the N-terminus of 53BP1; mutation of these sites abolishes TOPBP1, ATR, and CHK1 recruitment to 53BP1 damage foci and abrogates G1 cell cycle arrest; TOPBP1 interaction with 53BP1 is structurally complementary to its interaction with RAD9-RAD1-HUS1, allowing simultaneous binding and cooperation in ATR activation.\",\n      \"method\": \"Structural analysis, phospho-mutant analysis, co-IP, G1 checkpoint assay, immunofluorescence\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — structural data plus phospho-mutant functional analysis with ATR signaling readout\",\n      \"pmids\": [\"31135337\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TPX2/Aurora A heterodimer is a novel 53BP1 binding partner; TPX2/Aurora A counteracts 53BP1 function to promote DNA end resection, BRCA1/Rad51 recruitment, and HR; loss of TPX2 or Aurora A causes deprotection of stalled replication forks in an MRE11-dependent manner; concurrent 53BP1 loss rescues BRCA1/Rad51 recruitment and fork instability.\",\n      \"method\": \"Co-IP (MS), immunofluorescence, siRNA knockdown, replication fork protection assay, HR assay\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — MS-based co-IP plus functional rescue by 53BP1 loss; single lab\",\n      \"pmids\": [\"30602538\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"LC8 (DYNLL1) accumulates at laser-induced DNA damage tracks in a 53BP1-dependent manner, requiring the H2AX-MDC1-RNF8-RNF168 cascade; genetic inactivation of LC8 or its interaction with 53BP1 causes checkpoint defects; LC8 loss alleviates hypersensitivity of BRCA1-depleted cells to IR and PARP inhibition.\",\n      \"method\": \"Laser micro-irradiation, co-IP, LC8 genetic inactivation, checkpoint assay, PARPi sensitivity\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — localization plus genetic inactivation with checkpoint and PARPi readouts; single lab\",\n      \"pmids\": [\"30982887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Preformed 53BP1 dimers relocate from the nucleoplasm to DSB sites; at DSBs, consecutive recognition of H2AK15ub and H4K20me2 leads to assembly of 53BP1 oligomers and a mature foci structure, as quantified in living cells by fluorescence fluctuation spectroscopy.\",\n      \"method\": \"Fluorescence fluctuation spectroscopy (FFS), AsiSI-inducible DSB system, live-cell imaging\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — quantitative live-cell method establishing oligomerization dynamics at endogenous DSBs\",\n      \"pmids\": [\"33188174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"53BP1 localizes to replication forks following induced replication stress and is required for normal ATR-Chk1-p53 signaling; absence of 53BP1 leads to defective ATR-Chk1 signaling, caspase 3-mediated cell death, and degradation of nascent replicated DNA in early S-phase B cells.\",\n      \"method\": \"53BP1-/- primary B cells, replication fork labeling (EdU/BrdU), Chk1 phosphorylation assay, caspase activation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — KO primary cells with multiple mechanistic readouts; single lab\",\n      \"pmids\": [\"29378830\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PRMT5 methylates and stabilizes 53BP1 to promote NHEJ; Src kinase phosphorylates PRMT5 at Y324, suppressing PRMT5 methyltransferase activity and preventing 53BP1 methylation; Src-mediated inhibition of PRMT5 during DNA damage blocks NHEJ and leads to apoptosis.\",\n      \"method\": \"In vitro methylation assay, co-IP, phospho-mutant analysis, NHEJ reporter, apoptosis assay\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — in vitro methylation assay plus functional NHEJ assay; single lab\",\n      \"pmids\": [\"32759981\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NUDT16 regulates 53BP1 stability by reversing ADP-ribosylation; ADP-ribosylated 53BP1 is targeted by RNF146 for polyubiquitination and degradation; NUDT16 catalytic activity is required for 53BP1 de-ADP-ribosylation, stability, and localization at DSBs.\",\n      \"method\": \"ADP-ribosylation assay, ubiquitination assay, co-IP, NUDT16 catalytic mutant, immunofluorescence\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — biochemical modification assays plus localization functional readout; single lab\",\n      \"pmids\": [\"31911551\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Centrosome loss in neural progenitor cells prolongs mitosis and activates a 53BP1-USP28-TP53 mitotic surveillance pathway causing apoptosis; deletion of 53BP1 or USP28 restores NPC proliferation and brain size without correcting upstream centrosome defects, establishing 53BP1 as a required component of this pathway.\",\n      \"method\": \"Conditional KO mouse models, brain size measurement, mitotic timing assay, apoptosis assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis in multiple KO mouse models with clear developmental phenotype\",\n      \"pmids\": [\"33226141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ATM-phosphorylated SPOP undergoes a conformational change (revealed by crystal structure) that stabilizes its interaction with 53BP1; SPOP induces polyubiquitination of 53BP1, causing VCP/p97-mediated extraction of 53BP1 from chromatin during S phase, thus promoting HR over NHEJ; cancer-derived SPOP mutations block this interaction.\",\n      \"method\": \"X-ray crystal structure of SPOP, co-IP, ubiquitination assay, SPOP mutant analysis, HR/NHEJ reporter\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — crystal structure plus biochemical ubiquitination/co-IP and functional HR assay\",\n      \"pmids\": [\"34144977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"AHNAK binds the 53BP1 oligomerization domain in G1 phase and controls 53BP1 multimerization; loss of AHNAK leads to hyper-accumulation of 53BP1 on chromatin and enhanced phase separation, culminating in elevated p53 response.\",\n      \"method\": \"Co-IP, fluorescence microscopy, phase separation assay, p53 target gene expression, siRNA/KO\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — co-IP with domain mapping plus phase separation and functional p53 readout\",\n      \"pmids\": [\"33961796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TIRR inhibits formation of the 53BP1 Tudor domain-p53 K382me2 complex; loss of TIRR causes aberrant increases in p53 transactivation; TIRR binds the Tudor domain and blocks p53 dimethyl-lysine recognition, linking TIRR to cell-fate decisions beyond DSB repair.\",\n      \"method\": \"Co-IP, Tudor domain-p53 binding assay (methylated K382 peptide), p53 target gene expression, TIRR KO\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — biochemical binding assay plus functional gene expression readout and KO phenotype\",\n      \"pmids\": [\"33961797\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Lamin B1 directly interacts with 53BP1 and sequesters it from DSB sites; lamin B1 overexpression impedes 53BP1 recruitment to DNA damage, causes persistence of DNA damage, and defects in NHEJ; the interaction is dissociated after DNA damage.\",\n      \"method\": \"Co-IP, pulldown, immunofluorescence, NHEJ reporter, DSB sensitivity assay\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct co-IP plus functional NHEJ assay and localization; single lab\",\n      \"pmids\": [\"34452908\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"AMPK directly phosphorylates 53BP1 at Ser1317 in response to DSBs; this phosphorylation promotes 53BP1 recruitment to DSBs and efficient classical NHEJ (c-NHEJ), maintaining genomic stability and immune repertoire diversity.\",\n      \"method\": \"In vitro kinase assay (AMPK-53BP1), co-IP, phospho-mutant analysis, immunofluorescence, CSR assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro kinase assay plus phospho-mutant functional analysis; single lab\",\n      \"pmids\": [\"33596428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ATM phosphorylates ESCO2 at S196 and T233; MDC1 recognizes phosphorylated ESCO2 and recruits it to DSBs; ESCO2-mediated SMC3 acetylation stabilizes cohesin complex conformation and regulates chromatin structure at DSBs, which is essential for 53BP1 recruitment and formation of 53BP1 microdomains.\",\n      \"method\": \"Co-IP, acetylation assay, siRNA knockdown, immunofluorescence, ESCO2 KO cells/xenograft\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — co-IP plus biochemical acetylation and functional 53BP1 recruitment assay; single lab\",\n      \"pmids\": [\"37377435\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"53BP1 undergoes liquid-liquid phase separation with HP1α at heterochromatin in a mutually dependent manner; 53BP1 deletion reduces heterochromatin centers and de-represses tandem repetitive DNA; domains required for LLPS at heterochromatin overlap with but are distinct from those for DSB repair.\",\n      \"method\": \"LLPS assay, CRISPR KO, immunofluorescence, repeat RNA expression assay, domain deletion analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — LLPS assay plus KO phenotype and domain analysis; single lab\",\n      \"pmids\": [\"35042897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RIF1 is a phosphopeptide-binding protein that directly interacts with three phosphorylated 53BP1 epitopes sharing an LxL motif followed by two closely apposed phosphorylated residues; simultaneous mutation of these sites abrogates RIF1 IRIF but only fully compromises repair when an alternative shieldin recruitment mode is also disabled; RIF1 also modifies shieldin action independently of 53BP1 binding.\",\n      \"method\": \"Phosphopeptide binding assay, mutagenesis, co-IP, immunofluorescence (IRIF), CSR assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — phosphopeptide binding assay plus mutagenesis and functional assay revealing two RIF1 recruitment modes\",\n      \"pmids\": [\"35216668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thereby reducing DNA repair at DSBs.\",\n      \"method\": \"SARS-CoV-2 infection of cells and mice, 53BP1 foci quantification, lncRNA perturbation assay\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — viral protein expression with 53BP1 foci readout and mechanistic lncRNA link; single lab\",\n      \"pmids\": [\"36894671\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"53BP1 is recruited to DNA double-strand break (DSB) sites through its tandem Tudor domain binding dimethylated H4K20 (H4K20me2) and its UDR motif binding RNF168-catalyzed H2AK15ub on nucleosomes (structural basis resolved by cryo-EM); ATM phosphorylates 53BP1 to recruit the downstream effectors RIF1 (via phosphopeptide recognition of LxL-phospho motifs) and PTIP (via distinct phospho-sites), and RIF1 in turn recruits the shieldin complex (SHLD1-SHLD2-SHLD3-REV7), whose SHLD2 subunit binds single-stranded DNA to protect DNA ends; CST-Polα acts downstream of shieldin to perform fill-in synthesis that limits resection; this entire 53BP1-RIF1-shieldin-CST/Polα axis suppresses 5′ end resection, promotes NHEJ and class switch recombination, and opposes homologous recombination, while BRCA1 antagonizes 53BP1 signaling in S/G2 by inhibiting ATM-dependent 53BP1 phosphorylation; 53BP1 chromatin access is additionally regulated by TIRR (which masks the Tudor domain), SPOP-mediated polyubiquitination (which extracts 53BP1 from chromatin in S phase), acetylation of the UDR motif by CBP/HDAC2, ADP-ribosylation reversed by NUDT16, and sequestration by lamin B1 and NuMA; beyond DSB repair, 53BP1 phase separation amplifies p53 signaling, 53BP1 nuclear bodies restrain replication timing of under-replicated DNA, and 53BP1 participates in the mitotic surveillance pathway (with USP28 and TP53) to eliminate cells after prolonged mitosis.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"53BP1 is a central chromatin-based scaffold that directs DNA double-strand break repair pathway choice by promoting non-homologous end joining (NHEJ) and suppressing homologous recombination, while also amplifying p53 signaling and safeguarding genome integrity during replication and mitosis. Recruitment to DSBs requires bivalent nucleosome recognition — the tandem Tudor domain binds H4K20me2 while the UDR motif engages RNF168-catalyzed H2AK15ub, as revealed by cryo-EM — and this recognition is gated by regulators including TIRR (which masks the Tudor domain), SPOP-mediated ubiquitination (which extracts 53BP1 from chromatin in S phase), CBP/HDAC2-controlled UDR acetylation, and cell-cycle-dependent H4K20me2 dilution during replication [PMID:27462807, PMID:28241136, PMID:34144977, PMID:29190394, PMID:28564601]. ATM-dependent phosphorylation of 53BP1 recruits distinct effectors — RIF1 via LxL-phosphopeptide motifs and PTIP via separate phospho-sites — with RIF1 in turn recruiting the shieldin complex (SHLD1–SHLD2–SHLD3–REV7) and CST–Polα to protect DNA ends from resection and execute fill-in synthesis, collectively enabling class-switch recombination and long-range V(D)J joining [PMID:23727112, PMID:35216668, PMID:30022168, PMID:30022158, PMID:18931658]. Beyond DSB repair, 53BP1 undergoes liquid–liquid phase separation that concentrates p53 and amplifies its transcriptional output, forms nuclear bodies that restrain replication timing of under-replicated loci, and functions with USP28 and TP53 in a mitotic surveillance pathway that eliminates cells after prolonged mitosis [PMID:31267591, PMID:30804506, PMID:33226141].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing that 53BP1 is an ATM substrate that forms DNA-damage-induced nuclear foci answered the foundational question of how 53BP1 is activated in the damage response, placing it within the ATM signaling axis.\",\n      \"evidence\": \"Immunofluorescence, in vitro ATM kinase assay, ATM-deficient human cells and Xenopus extracts\",\n      \"pmids\": [\"11331310\", \"11238909\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream substrates/effectors of 53BP1 phosphorylation unknown\", \"Whether foci formation requires direct chromatin binding or indirect recruitment unresolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstrating that 53BP1 recruitment depends on γH2AX identified the chromatin mark that seeds 53BP1 accumulation, resolving how the damage signal spreads to recruit repair factors.\",\n      \"evidence\": \"In vitro binding assay with phosphorylated/unphosphorylated H2AX; reconstitution in H2AX-deficient cells\",\n      \"pmids\": [\"12697768\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether γH2AX binding is direct via the BRCT domain versus indirect via MDC1 not yet distinguished\", \"Tudor domain–histone methylation recognition not yet discovered\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Knockout studies revealed that 53BP1 promotes long-range DNA end joining during V(D)J recombination and that MDC1 acts as an intermediary between γH2AX and 53BP1, defining 53BP1's physiological role in lymphocyte genome rearrangement.\",\n      \"evidence\": \"53BP1 KO mice with V(D)J joining defects; MDC1–53BP1 co-IP and recruitment epistasis in H2AX/MDC1-deficient cells\",\n      \"pmids\": [\"18931658\", \"18986980\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of DNA end protection unknown\", \"Whether 53BP1 physically prevents resection or acts indirectly unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Discovery that MMSET-deposited H4K20me2 at DSBs recruits 53BP1, together with the finding that oligomerization and ATM phosphorylation are both needed for CSR, established that 53BP1 uses a histone-methylation-reading mechanism distinct from γH2AX and that multiple 53BP1 features cooperate in repair.\",\n      \"evidence\": \"H4K20me2 ChIP at DSBs with MMSET knockdown; 53BP1 structural mutants tested in quantitative CSR and paired-DSB joining assays\",\n      \"pmids\": [\"21293379\", \"21549309\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether H4K20me2 is read by the Tudor domain directly not structurally confirmed\", \"Effector proteins downstream of 53BP1 phosphorylation not yet identified\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Phosphomutant knock-in mice and biochemical studies separated 53BP1's effector arms: ATM-phosphorylated S/TQ sites recruit RIF1 for end-blocking while distinct sites recruit PTIP for productive CSR; concurrently, RNF168-catalyzed K63-ubiquitylation of 53BP1 was shown to be required for initial recruitment, and H4K16 acetylation was identified as an antagonist of H4K20me2 binding.\",\n      \"evidence\": \"53BP1 phosphomutant knock-in mice with CSR/NHEJ/HR readouts; RNF168 KO ubiquitylation assays; H4K16ac chromatin fractionation and NHEJ reporter\",\n      \"pmids\": [\"23727112\", \"24324146\", \"23329852\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of dual histone-mark recognition unresolved\", \"Identity of end-protection effectors downstream of RIF1 unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"The cryo-EM structure of 53BP1 bound to ubiquitylated-methylated nucleosomes resolved the long-standing question of how 53BP1 simultaneously reads H4K20me2 (Tudor domain) and H2AK15ub (UDR motif), revealing selectivity determinants including arginine fingers and acidic-patch contacts.\",\n      \"evidence\": \"Cryo-EM at 4.5 Å of 53BP1 dimer on reconstituted NCP-ubme nucleosome\",\n      \"pmids\": [\"27462807\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How higher-order oligomerization relates to foci maturation not shown structurally\", \"Mechanism by which BRCA1 displaces 53BP1 in S/G2 structurally unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Multiple regulatory layers of Tudor domain access were uncovered: TIRR was identified as a Tudor-masking protein whose dissociation is ATM-dependent; H4K20me2 dilution during replication was shown to limit 53BP1 accumulation in S phase; and competitors RNF169/RAD18 were shown to displace 53BP1 from ubiquitylated nucleosomes.\",\n      \"evidence\": \"TIRR co-IP and competition binding; crystal structure of TIRR–Tudor complex at 1.76 Å; cell-cycle H4K20me2 ChIP with EdU; NMR of RNF169/RAD18–NCP-ubme competition\",\n      \"pmids\": [\"28241136\", \"29844495\", \"28564601\", \"28506460\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signal that releases TIRR in vivo not fully defined\", \"Quantitative contribution of each gating mechanism to pathway choice not measured\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The shieldin complex (SHLD1–SHLD2–SHLD3–REV7) and downstream CST–Polα were identified as the missing effectors that explain how 53BP1–RIF1 physically blocks end resection, with SHLD2 OB-folds binding ssDNA and Polα performing fill-in synthesis; loss of shieldin confers PARPi resistance in BRCA1-deficient cells.\",\n      \"evidence\": \"Proteomic identification; co-IP and genetic KO; ssDNA binding assays; CSR and PARPi sensitivity assays across multiple concurrent studies\",\n      \"pmids\": [\"30022168\", \"30022158\", \"30046110\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of shieldin assembly and ssDNA engagement unknown at atomic level\", \"Whether CST–Polα acts at all 53BP1-dependent repair events or only CSR unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Additional modulators of 53BP1 chromatin occupancy were defined: CBP acetylation of the UDR motif blocks nucleosome binding (reversed by HDAC2), DYNLL1 promotes 53BP1 oligomerization, and BRCA1 inhibits ATM-dependent 53BP1 phosphorylation in S/G2 to favor HR.\",\n      \"evidence\": \"Acetylation assay and NHEJ/HR reporters; DYNLL1 KO mice with CSR assay; cell-cycle-sorted phospho-specific IF with BRCA1 domain mutants\",\n      \"pmids\": [\"29190394\", \"30559443\", \"27462418\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How BRCA1 mechanistically inhibits ATM phosphorylation of 53BP1 remains unclear\", \"Whether acetylation and DYNLL1 regulation are coupled not tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"53BP1 was shown to enforce two mechanistically separable anti-HR blocks (a pre-resection block via PTIP/S25 and a post-resection block via shieldin), and to form nuclear bodies in G1 daughters that restrain replication timing of under-replicated loci, revealing functions beyond acute DSB repair.\",\n      \"evidence\": \"53BP1-S25A knock-in × BRCA1Δ11 mice with epistasis; live-cell replication timing analysis of 53BP1-NB-associated loci\",\n      \"pmids\": [\"31653568\", \"30804506\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How 53BP1-NBs sense under-replicated DNA is unknown\", \"Whether the two anti-HR blocks are independently regulated in different tissues unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"53BP1 liquid–liquid phase separation was shown to concentrate p53 and amplify its transcriptional response, establishing that 53BP1 foci are condensates with signaling function beyond structural scaffolding.\",\n      \"evidence\": \"OptoDroplet experiments, endogenous CRISPR tagging, osmotic/chemical perturbation, p53 target gene expression\",\n      \"pmids\": [\"31267591\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which phase-separation-competent domains are essential in vivo unclear\", \"Relationship between LLPS and chromatin-bound oligomers not mechanistically separated\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"53BP1 was placed in a mitotic surveillance pathway with USP28 and TP53 that eliminates neural progenitor cells after prolonged mitosis; NUDT16-mediated de-ADP-ribosylation was found to stabilize 53BP1 by preventing RNF146-dependent degradation.\",\n      \"evidence\": \"Conditional triple KO mice with brain size rescue; ADP-ribosylation/ubiquitination assays with NUDT16 catalytic mutants\",\n      \"pmids\": [\"33226141\", \"31911551\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How 53BP1 senses prolonged mitosis mechanistically unresolved\", \"Whether ADP-ribosylation regulates 53BP1 at DSBs or only governs steady-state levels unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Structural and biochemical work showed that SPOP phosphorylation by ATM induces conformational opening that enables 53BP1 polyubiquitination and VCP-mediated chromatin extraction in S phase; TIRR was further shown to block Tudor–p53-K382me2 recognition, linking TIRR to cell-fate signaling; AHNAK was identified as an oligomerization regulator controlling 53BP1 phase separation and p53 output.\",\n      \"evidence\": \"SPOP crystal structure, ubiquitination and HR assay; TIRR–Tudor–p53-K382me2 binding assay; AHNAK co-IP and phase separation assay\",\n      \"pmids\": [\"34144977\", \"33961797\", \"33961796\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cancer-derived SPOP mutations' effects on 53BP1-dependent repair in patient tumors not validated\", \"How AHNAK itself is regulated during DSB signaling unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The structural code for RIF1 recruitment was resolved: RIF1 is a phosphopeptide-binding protein recognizing three LxL-phospho motifs in 53BP1, with an alternative shieldin recruitment mode providing redundancy; 53BP1 was also shown to phase-separate with HP1α at heterochromatin to maintain repeat silencing.\",\n      \"evidence\": \"Phosphopeptide binding assay with mutagenesis and CSR; LLPS assay with CRISPR KO and repeat RNA expression\",\n      \"pmids\": [\"35216668\", \"35042897\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of full-length RIF1–53BP1 complex not determined\", \"Whether heterochromatin LLPS function is independent of DSB repair in vivo unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: the structural basis of 53BP1 higher-order oligomerization at DSBs; how 53BP1 senses prolonged mitosis in the surveillance pathway; whether distinct post-translational modifications (ADP-ribosylation, methylation, acetylation) cooperate or act in separate contexts; and the full mechanism by which BRCA1 inhibits ATM-dependent 53BP1 phosphorylation.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structure of full-length 53BP1 oligomer on chromatin\", \"Mitotic surveillance sensing mechanism unknown\", \"Integrated PTM code for 53BP1 not systematically tested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [9, 13, 14, 19, 24]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [10, 26, 27, 32, 49]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [0, 1, 37]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [19, 24, 42]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [33, 48]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [3, 8, 10, 19, 26, 27, 32]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 10, 28]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [7, 34, 41]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [41]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [19, 48]}\n    ],\n    \"complexes\": [\n      \"53BP1-RIF1-shieldin (SHLD1-SHLD2-SHLD3-REV7)\",\n      \"53BP1-TIRR\"\n    ],\n    \"partners\": [\n      \"RIF1\",\n      \"SHLD2\",\n      \"REV7\",\n      \"TIRR\",\n      \"DYNLL1\",\n      \"PTIP\",\n      \"TOPBP1\",\n      \"AHNAK\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}