Affinage

CTCF

Transcriptional repressor CTCF · UniProt P49711

Length
727 aa
Mass
82.8 kDa
Annotated
2026-06-09
100 papers in source corpus 43 papers cited in narrative 43 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 9/9 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CTCF is the principal architectural regulator of mammalian genome folding, an 11-zinc-finger DNA-binding protein that establishes topologically associating domain (TAD) boundaries and directs chromatin loops while genome compartmentalization persists independently of its activity (PMID:28525758). Crystal structures show ZF1–ZF7 reading triplet base pairs along the DNA major groove and ZF8 acting as a minor-groove spacer that positions ZF9–ZF11 for cross-strand contacts, defining the basis of cognate-site recognition (PMID:37439339). CTCF operates by acting as a polar barrier to cohesin-mediated loop extrusion: convergent binding-site orientation is required for loop formation (PMID:26527277), and an N-terminal motif blocks cohesin translocation only when it faces the complex by docking onto the STAG1 subunit, whereas a C-terminally oriented CTCF instead accelerates cohesin compaction (PMID:37536339, PMID:31937660). In reconstituted single-molecule systems CTCF is sufficient to halt diffusing and extruding cohesin in a DNA-tension-dependent manner and actively reverses extrusion direction (PMID:37076620). CTCF binds chromatin far more dynamically than cohesin and the fully looped state is rare and short-lived, so individual CTCF boundaries rather than stable loops are the operative regulatory units (PMID:28467304, PMID:35420890, PMID:36471076). CTCF chromatin engagement is gated by multiple inputs: DNA methylation blocks binding (PMID:32333838), poly(ADP-ribosyl)ation is required for insulator function (PMID:15361875), LATS-kinase phosphorylation of zinc-finger linkers dissociates CTCF from stress-responsive loci (PMID:32128389), RNA contacts through ZF1/ZF10 are structurally required for looping (PMID:31522988), R-loop-associated G-quadruplexes promote binding (PMID:37552993, PMID:34209337), and the NURF/BPTF remodeler opens nucleosomes to license occupancy (PMID:38816647). Beyond architecture, CTCF directly controls transcription—suppressing upstream antisense initiation at divergent promoters independently of looping (PMID:36369346), regulating RNAP II pausing and elongation via DSIF, NELF and P-TEFb recruitment (PMID:26399478), and acting as a conventional activator at a subset of genes (PMID:34453048). It directs cell-type-specific programs by cooperating with lineage-specific pioneer factors and the cohesin cofactor MAZ, and is required for cortical interneuron specification and, with its paralog BORIS/CTCFL, for spermatogenesis (PMID:35145304, PMID:37851578, PMID:30377227, PMID:34158481). Loss of CTCF boundary insulation enables enhancer–oncogene activation, as shown by TAD fusion driving FGF3 induction (PMID:38452764).

Mechanistic history

Synthesis pass · year-by-year structured walk · 22 steps
  1. 2004 High

    Established that a post-translational modification, poly(ADP-ribosyl)ation, is functionally required for CTCF insulator activity rather than merely correlated with bound sites.

    Evidence ChIP, ChIP-on-chip and insulator-trap assays with PARP inhibition at the H19 ICR and >140 CTCF sites

    PMID:15361875

    Open questions at the time
    • Does not identify the modified residues or PARP enzyme
    • Mechanism linking PARylation to insulation not resolved
  2. 2015 High

    Showed that loop formation depends not just on CTCF binding but on the orientation of its recognition motif, revealing binding polarity as a determinant of higher-order structure.

    Evidence CRISPR/Cas9 deletion and oriented re-insertion of CTCF sites with 4C-seq and ChIP-seq

    PMID:26527277

    Open questions at the time
    • Did not explain the structural basis of polarity
    • Cohesin recruitment was restored without loops, leaving the mechanism unresolved at the time
  3. 2017 High

    Demonstrated that CTCF is acutely and dose-dependently required for TAD insulation and looping but not for A/B compartmentalization, separating loop-level from compartment-level genome organization.

    Evidence Auxin-inducible degron in mouse ESCs with Hi-C and ChIP-seq

    PMID:28525758

    Open questions at the time
    • Did not address the kinetics or biochemistry of how CTCF blocks cohesin
    • Compartment-driving factors left unidentified
  4. 2017 High

    Resolved that CTCF binds chromatin transiently while cohesin is long-lived, implying loops are dynamic structures that frequently break and reform.

    Evidence Single-molecule live-cell imaging combined with co-IP and ChIP-seq

    PMID:28467304

    Open questions at the time
    • Did not quantify the actual looped fraction in single cells
    • Stoichiometry of bound complexes not measured
  5. 2019 High

    Identified RNA interaction through ZF1/ZF10 as a structural requirement for CTCF-mediated genome organization distinct from DNA binding.

    Evidence ZF1/ZF10 site-directed mutagenesis with Hi-C, ChIP-seq and transcription inhibition

    PMID:31522988

    Open questions at the time
    • Specific RNA species mediating loops not defined
    • How RNA promotes clustering mechanistically unresolved
  6. 2019 High

    Provided absolute copy numbers of CTCF and cohesin, indicating many enrichment sites are unoccupied in any single cell and that loops form stochastically.

    Evidence Mass spectrometry, FCS and FRAP integrated with ChIP-seq in HeLa cells

    PMID:31204999

    Open questions at the time
    • Stoichiometry measured in one cell type
    • Does not directly visualize loop dynamics
  7. 2020 High

    Localized the cohesin-anchoring activity to a 79-aa N-terminal region of CTCF and showed it is necessary but not autonomously sufficient, with the first two zinc fingers and 3D geometry also contributing.

    Evidence Domain-swap and CTCF–BORIS chimera mutagenesis with cohesin ChIP-seq and Hi-C

    PMID:31937660

    Open questions at the time
    • Atomic interface with cohesin not yet defined at this stage
    • Contribution of geometry vs. sequence not fully separated
  8. 2020 High

    Connected a signaling kinase to genome architecture by showing LATS phosphorylates CTCF zinc-finger linkers to selectively dissociate it from stress-responsive boundaries.

    Evidence Kinase assays, mass spectrometry, stress-induced ChIP-seq and Hi-C

    PMID:32128389

    Open questions at the time
    • Generality of LATS regulation across boundaries unclear
    • Upstream stress inputs only partly defined
  9. 2020 High

    Defined a DNA-methylation→CTCF→cohesin→loop axis controlling alternative polyadenylation, linking epigenetic state to RNA processing through architecture.

    Evidence CTCF ChIP-seq, CRISPR site deletion, RAD21 depletion and polyA profiling with WGBS

    PMID:32333838

    Open questions at the time
    • Breadth of polyA regulation by CTCF loops not established
    • Causal sufficiency of methylation alone not isolated
  10. 2021 High

    Identified Jpx RNA as a CTCF release factor that competitively displaces CTCF from low-affinity sites to set anchor selectivity.

    Evidence Jpx depletion with CTCF ChIP-seq, Hi-C, RNA-seq and competitive binding assays

    PMID:34856126

    Open questions at the time
    • Direct biochemical mode of competitive displacement only partly defined
    • Generality beyond developmentally sensitive sites unclear
  11. 2021 High

    Showed CTCF is required for post-mitotic re-formation of domain boundaries and that at some genes CTCF acts as a conventional transcriptional activator independent of architecture.

    Evidence Mitosis-timed auxin degradation with Hi-C and RNA-seq in erythroid cells

    PMID:34453048

    Open questions at the time
    • Activator mechanism distinct from looping not molecularly defined
    • Which genes use architectural vs. direct activation not generalized
  12. 2021 High

    Demonstrated with the paralog BORIS that CTCF binding at heterodimeric sites is required for spermatogenesis, defining a developmental requirement and paralog cooperation.

    Evidence Compound Ctcf/Boris mouse mutants with CTCF ChIP-seq, RNA-seq and fertility assays

    PMID:34158481

    Open questions at the time
    • Molecular nature of CTCF–BORIS heterodimer interface not defined
    • Tissue specificity of heterodimer sites not fully mapped
  13. 2021 Medium

    Showed CTCF depletion in pluripotent cells reversibly promotes a 2C-like state via DNA damage at CTCF sites and ZSCAN4 activation, linking architecture to totipotency control.

    Evidence Auxin-degron CTCF depletion with flow cytometry, RNA-seq and ChIP-seq

    PMID:34381034

    Open questions at the time
    • Causal link between DNA damage and reprogramming not fully resolved
    • Cell-type specificity mechanism unexplained
  14. 2022 High

    Directly quantified that CTCF-anchored loops are rare and short-lived, refining the model toward single boundaries as primary regulators.

    Evidence Super-resolution live-cell imaging of the Fbn2 TAD with Bayesian inference

    PMID:35420890

    Open questions at the time
    • Generalizability of loop lifetimes to other loci unknown
    • Functional output of transient single boundaries not measured here
  15. 2022 High

    Identified MAZ as a CTCF boundary cofactor that contacts RAD21 and is required for Hox cluster insulation in vivo.

    Evidence Genome-wide CRISPR screen, co-IP, ChIP-seq, Hi-C and mouse motif deletions

    PMID:35145304

    Open questions at the time
    • Whether MAZ acts at boundaries genome-wide not established
    • Mechanism of MAZ–RAD21 cooperation with CTCF not resolved
  16. 2022 High

    Separated CTCF's architectural role from a direct transcriptional function by showing it suppresses upstream antisense initiation at divergent promoters.

    Evidence Acute CTCF degradation with nascent transcription, RNA-FISH and genome editing

    PMID:36369346

    Open questions at the time
    • Molecular mechanism of antisense suppression not defined
    • Breadth across promoter classes not fully mapped
  17. 2022 High

    Distinguished two cohesin populations by ring integrity, showing CTCF-anchored loops are lost on RAD21 cleavage whereas intra-domain loops resist, revealing distinct loop mechanisms.

    Evidence Engineered cleavable RAD21 in isolated nuclei with Hi-C and cohesin ChIP-seq

    PMID:36202971

    Open questions at the time
    • Structural basis of the two cohesin states not resolved
    • How CTCF stabilizes its cohesin population biochemically unclear
  18. 2023 High

    Provided the structural and biophysical basis for CTCF polarity by showing the N-terminal motif blocks cohesin only when facing it, docking on STAG1, while reversed CTCF accelerates compaction.

    Evidence Cryo-EM of the cohesin–CTCF complex with single-molecule imaging and mutagenesis

    PMID:37536339

    Open questions at the time
    • Dynamics of barrier engagement during extrusion not fully captured
    • Role of additional CTCF domains in the structure not detailed
  19. 2023 High

    Reconstituted CTCF as an active, tension-dependent and directional barrier that reverses cohesin extrusion rather than a passive block.

    Evidence In vitro single-molecule imaging of CTCF–cohesin on DNA

    PMID:37076620

    Open questions at the time
    • In-cell relevance of tension-dependence not directly measured
    • Quantitative contribution of direction reversal to TADs unclear
  20. 2023 High

    Defined the DNA-recognition architecture of all 11 zinc fingers, explaining how CTCF reads its composite motif.

    Evidence X-ray crystal structures of CTCF–DNA complexes spanning CORE and flanking motifs

    PMID:37439339

    Open questions at the time
    • Does not address RNA or G4 binding interfaces
    • Structural effect of methylation on binding not captured
  21. 2023 High

    Established R-loop-associated G-quadruplexes as promoters of CTCF binding, adding a nucleic-acid-structure input to occupancy control.

    Evidence In vitro binding, DRIP, G4-seq, R-loop attenuation, G4 stabilization and CRISPR deletion

    PMID:37552993

    Open questions at the time
    • Fraction of genome-wide sites dependent on G4s not quantified
    • How G4 binding integrates with motif recognition unresolved
  22. 2024 High

    Demonstrated causally that disrupting a CTCF boundary fuses TADs and activates an oncogene through modest changes in enhancer–promoter contact frequency.

    Evidence CRISPR deletion of four CTCF motifs with micro-C and RNA-seq, compared to patient data

    PMID:38452764

    Open questions at the time
    • Generality of small contact-change-to-large-expression coupling unclear
    • Boundary-disruption frequency in disease not established here

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the many gating inputs (methylation, PARylation, phosphorylation, RNA, G4s, remodelers) are integrated in real time at individual sites to produce the rare, transient loops observed, and how architectural versus direct transcriptional functions are partitioned genome-wide, remains unresolved.
  • No unified model integrating competing occupancy regulators
  • Architectural vs. transcriptional CTCF functions not separable at scale
  • In-cell biophysical barrier behavior not directly measured

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 3 GO:0003723 RNA binding 3 GO:0140110 transcription regulator activity 3 GO:0060090 molecular adaptor activity 2
Localization
GO:0005634 nucleus 3 GO:0000228 nuclear chromosome 2 GO:0005635 nuclear envelope 2
Pathway
R-HSA-1266738 Developmental Biology 3 R-HSA-4839726 Chromatin organization 3 R-HSA-74160 Gene expression (Transcription) 3 R-HSA-1643685 Disease 2
Partners
BORISBPTFMAZMYCRAD21SMARCA5STAG1TRF2
Complex memberships
cohesin-CTCF complex

Evidence

Reading pass · 43 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 Acute auxin-inducible degradation of CTCF in mouse embryonic stem cells demonstrated that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). CTCF loss abolished TAD boundaries but active/inactive genome compartmentalization remained intact, showing compartmentalization emerges independently of TAD insulation. CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Auxin-inducible degron system (AID) in mouse ESCs combined with Hi-C and ChIP-seq Cell High 28525758
2015 CTCF binding polarity (orientation of the recognition sequence) determines chromatin loop formation. CRISPR/Cas9 deletion of core CTCF binding sites abolished CTCF and cohesin recruitment and disrupted loops with convergent distal CTCF sites. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment but did not re-establish chromatin loops, demonstrating that binding polarity is functionally required for higher-order chromatin structure. CRISPR/Cas9 genome editing combined with 4C-seq and ChIP-seq Molecular cell High 26527277
2023 In vitro single-molecule imaging showed that CTCF is sufficient to block both diffusing and loop-extruding cohesin, functioning as a DNA-tension-dependent barrier. CTCF acts asymmetrically consistent with its role in TAD boundary formation, and actively regulates cohesin's loop-extrusion activity by changing its direction and inducing loop shrinkage, rather than being a passive barrier. Single-molecule imaging of CTCF and cohesin interactions on DNA in vitro; reconstituted system Nature High 37076620
2023 Cryo-EM structure of the cohesin-CTCF complex revealed that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping by reaching its binding site on the STAG1 cohesin subunit only when the CTCF N-terminus faces cohesin, explaining the polarity requirement. Single-molecule imaging confirmed that this N-terminal motif blocks cohesin-mediated DNA compaction. A C-terminally oriented CTCF instead accelerates DNA compaction by cohesin. Cryo-EM structure determination combined with single-molecule imaging and biochemical assays Molecular cell High 37536339
2023 Crystal structures of human CTCF including all 11 zinc fingers in complex with DNA containing CORE, 5' upstream, and 3' downstream motifs revealed that ZF1–ZF7 follow the right-handed twist of DNA recognizing triplet base pairs in the major groove, while ZF8 acts as a spacer across the DNA minor groove positioning ZF9–ZF11 to make cross-strand contacts with DNA. Basic residues in ZF8 form salt bridges with DNA phosphates in the minor groove. X-ray crystallography (crystal structures) of CTCF–DNA complexes Nucleic acids research High 37439339
2017 Single-molecule live-cell imaging showed that CTCF binds chromatin much more dynamically than cohesin (~1–2 min residence time vs. ~22 min for cohesin). After unbinding, CTCF quickly searches for another cognate site (~1 min) unlike cohesin (~33 min). Co-immunoprecipitation confirmed CTCF and cohesin co-occupy the same sites and form a biochemically stable complex, yet functionally act as a rapidly exchanging dynamic complex, implying chromatin loops are dynamic and frequently break and reform. Single-molecule imaging (live cell) combined with genomic ChIP-seq and biochemical co-IP eLife High 28467304
2022 Super-resolution live-cell imaging of the Fbn2 TAD in mouse ESCs showed that CTCF-anchored loops are rare and dynamic: the looped fraction was ~3–6.5% and median loop lifetime ~10–30 min. ~92% of the time cohesin-extruded loops exist within the TAD without bridging both CTCF boundaries, suggesting single CTCF boundaries rather than the fully looped state are the primary regulators. Super-resolution live-cell imaging with Bayesian inference quantification Science High 35420890
2004 CTCF carries the post-translational modification poly(ADP-ribosyl)ation (PARylation). ChIP analysis showed the PARylation mark segregates with the maternal allele of the H19 imprinting control region in a CTCF-binding-dependent manner. ChIP-on-chip extended this to >140 CTCF target sites. Inhibition of PARP activity with 3-aminobenzamide disrupted insulator function at most tested CTCF sites, establishing PARylation as required for CTCF-mediated chromatin insulation. ChIP, ChIP-on-chip, insulator trap assay with PARP inhibitor 3-aminobenzamide Nature genetics High 15361875
2020 A 79-amino-acid region within the CTCF N-terminus is essential for cohesin positioning at CTCF binding sites and chromatin loop formation. Fusing the CTCF N-terminus to artificial zinc fingers was not sufficient to redirect cohesin to non-CTCF sites, indicating no autonomously functioning cohesin-recruitment domain. The first two CTCF zinc fingers and the 3D geometry of CTCF–DNA complexes also contribute to cohesin retention. BORIS (CTCFL), lacking the relevant N-terminus, cannot anchor cohesin; converting BORIS to include the CTCF N-terminus and first two ZFs enabled cohesin positioning. Domain-swap mutagenesis, CTCF–BORIS chimeric constructs, ChIP-seq for cohesin positioning, Hi-C for loop formation Proceedings of the National Academy of Sciences of the United States of America High 31937660
2019 CTCF-RNA interactions are essential for genome organization. Mutations in zinc finger 1 (ZF1) or zinc finger 10 (ZF10) — which are not required for cognate DNA binding — disrupt CTCF association with endogenous RNAs, abolish chromatin loop formation, and impair chromatin domain insulation and long-range CTCF interactions. Inhibition of transcription also disrupts CTCF–chromatin association, indicating RNA interactions are a structural component of CTCF-mediated genome organization. Site-directed mutagenesis of ZF1/ZF10 combined with Hi-C, ChIP-seq, and transcription inhibition experiments in cells Molecular cell High 31522988
2020 LATS kinases phosphorylate CTCF in the zinc finger linkers, disabling DNA-binding activity. Cellular stress induces LATS nuclear translocation and CTCF ZF linker phosphorylation, selectively dissociating CTCF from a subset of genomic binding sites enriched at boundaries of chromatin domains containing LATS signaling target genes. Loss of CTCF binding at these sites disrupts local chromatin domains and downregulates genes within them. Kinase assays, mass spectrometry, ChIP-seq before/after stress in LATS-dependent manner, Hi-C Science advances High 32128389
2022 MAZ (Myc-associated zinc-finger protein) was identified as a cofactor of CTCF at chromatin borders in Hox gene clusters. MAZ colocalizes with CTCF at chromatin borders and interacts with the cohesin subunit RAD21. MAZ knockout disrupts gene expression and local TAD contacts. MAZ motif deletions phenocopy CTCF motif deletions, causing derepression of posterior Hox genes and homeotic transformations in mice. Genome-wide CRISPR knockout screen, co-immunoprecipitation, ChIP-seq, Hi-C, mouse genetic models Nature genetics High 35145304
2021 Jpx RNA functions as a CTCF release factor that determines anchor site selectivity. Jpx RNA targets thousands of genomic sites and displaces CTCF protein through competitive inhibition. Depletion of Jpx causes ectopic CTCF binding, massive shifts in chromosome looping, and downregulation of >700 Jpx target genes. Jpx selectively acts at low-affinity CTCF motifs at developmentally sensitive sites. Jpx RNA depletion (siRNA/ASO), CTCF ChIP-seq, Hi-C, RNA-seq, competitive binding assays Cell High 34856126
2020 Removal of DNA methylation enables CTCF binding, which recruits the cohesin complex, forming chromatin loops that promote proximal polyadenylation site usage. Deletion of the CTCF binding site or depletion of RAD21 cohesin subunit both restore distal polyadenylation site usage, establishing a DNA methylation → CTCF binding → cohesin recruitment → chromatin looping → alternative polyadenylation regulatory axis. CTCF ChIP-seq, CTCF site CRISPR deletion, RAD21 depletion, polyadenylation site profiling, whole-genome bisulfite sequencing Molecular cell High 32333838
2022 CTCF suppresses antisense (upstream antisense) transcription initiation at hundreds of divergent promoters in a manner independent of its architectural/looping function. Acute CTCF degradation increases antisense burst fraction but not sense transcription. Precisely positioned CTCF directly suppresses upstream antisense transcript initiation, as determined by genome editing, chromatin conformation studies, and high-resolution transcript mapping. Acute CTCF degradation (AID), nascent transcription measurements, RNA-FISH, genome editing, chromatin conformation capture Nature structural & molecular biology High 36369346
2019 CTCF confers nucleosome resilience at its binding sites: it displaces nucleosomes from its binding site and locally organizes large, phased nucleosomal arrays not only in interphase but also immediately after DNA replication and during mitosis. This nucleosome-positioning activity persists through the cell cycle and is associated with fast gene reactivation following replication and mitosis. MNase-seq and ATAC-seq in mouse ESCs at defined cell-cycle stages (post-replication, mitosis), correlation with CTCF ChIP-seq eLife Medium 31599722
2021 CTCF regulates RNAP II pausing and transcription elongation at the c-myc gene and termination at U2 snRNA genes. CTCF knockdown abrogates RNAP II pausing at the c-myc early elongation checkpoint by affecting DSIF recruitment, and causes a termination defect on U2 genes by affecting NELF recruitment. CTCF is also required for recruitment of P-TEFb, which phosphorylates NELF, DSIF, and RNAP II CTD Ser2 to activate elongation. CTCF siRNA knockdown, ChIP for RNAP II, DSIF, NELF and P-TEFb, in cells Transcription Medium 26399478
2019 An alternatively spliced shorter CTCF isoform (CTCF-s, skipping exons 3–4) competes with canonical CTCF for genome binding at similar DNA sequences. CTCF-s binding disrupts CTCF/cohesin occupancy, alters CTCF-mediated chromatin looping, and promotes apoptosis by enabling an abnormal long-range enhancer–promoter interaction at the IFI6 locus. ChIP-seq for CTCF-s vs. canonical CTCF, Hi-C, RNA-seq, overexpression in cells Nature communications Medium 30948729
2019 NPM1c (the AML frameshift mutant of NPM1 bearing a nuclear export signal) interacts with CTCF via the amino terminus of CTCF and the last 50 amino acids of NPM1c, causing cytoplasmic mislocalization of CTCF. Interfering with the NPM1c–CTCF interaction relocates CTCF back to the nucleus. Co-immunoprecipitation, subcellular fractionation/localization, domain mapping with truncation constructs Leukemia Medium 31831844
2022 CTCF and cohesin contribute to focal detachment of DNA from the nuclear lamina at CTCF binding sites within LADs, maintaining local chromatin accessibility at these sites. However, CTCF and cohesin are not primary determinants of LAD boundary positioning; LADs are maintained after CTCF/cohesin depletion. CTCF and cohesin reinforce but do not create LAD borders. DamID genome-nuclear lamina mapping before/after acute CTCF and cohesin depletion in mouse ESCs, ATAC-seq Genome biology Medium 36050765
2014 Vigilin (a multi-KH-domain protein) was identified as a binding partner of CTCF by yeast two-hybrid screening, confirmed by co-immunoprecipitation and GST pulldown. Vigilin is present at known CTCF target sites including the Igf2/H19 locus. CTCF knockdown reduces vigilin binding to the H19 imprinting control region (but not vice versa). The CTCF–vigilin complex contributes to reciprocal regulation of Igf2/H19 imprinting. Yeast two-hybrid, co-immunoprecipitation, GST pulldown, ChIP, knockdown The FEBS journal Medium 24725430
2023 R-loops facilitate CTCF binding through formation of associated G-quadruplex (G4) structures. R-loops and G4s co-localize with CTCF genomic sites in mouse ESCs. G4s promote CTCF binding to its cognate DNA motif in vitro. R-loop attenuation reduces CTCF binding in vivo. Deletion of a specific G4-forming sequence reduces CTCF binding and alters gene expression. Chemical stabilization of G4s increases CTCF occupancy and alters chromatin organization. In vitro binding assays, ChIP-seq, R-loop mapping (DRIP), G4-seq, G4 stabilization/depletion, CRISPR deletion Molecular cell High 37552993
2021 CTCF binding sites within active gene bodies can mediate chromatin loops between promoters and intragenic regions that promote alternative exon inclusion. Statistical analysis of CTCF ChIP-seq, Hi-C, and genotype data in a human cohort showed that inter-individual variability in CTCF binding at intragenic sites correlates with exon usage; exons in physical proximity to their promoters via CTCF loops are more included in spliced mRNA. Integrative analysis of CTCF ChIP-seq, Hi-C, RNA-seq, and genotype data across individuals (population-scale QTL-type analysis) Cell systems Low 29199022
2022 CTCF depletion during M-to-G1 phase transition impairs chromatin domain boundary re-formation after mitosis and prevents structural loop formation, leading to illegitimate contacts between cis-regulatory elements. Transient CRE contacts that are normally resolved after telophase persist in CTCF-depleted cells. At genes whose expression declines upon CTCF loss, CTCF functions as a conventional transcriptional activator independent of its architectural role. Acute CTCF degradation (AID) timed to mitosis, Hi-C, RNA-seq in mouse erythroid cells Nature communications High 34453048
2018 CTCF binds to enhancer RNAs in breast cancer cells stimulated with estrogen. CTCF binding to enhancer regions prevents Estrogen Receptor (ER) chromatin binding and hinders formation of additional ER-mediated enhancer–promoter loops, limiting induction of ER target genes. CTCF at the nuclear lamina interacts with enhancer regions to constrain ER loop formation; estrogen-ER promotes chromatin loops that contact the nuclear lamina where CTCF is present. RIP for CTCF–RNA interaction, ChIP-seq for CTCF/ER, 3C/ChIA-PET for looping, CTCF knockdown, nuclear lamina fractionation Nucleic acids research Medium 27638884
2021 CTCF depletion in ESCs promotes spontaneous conversion to a 2C-like (totipotent-like) state in a reversible manner. Forced 2C-like conversion by DUX is associated with DNA damage at a subset of CTCF binding sites. This phenotypic reprogramming is specific to pluripotent cells; neural progenitor cells do not show 2C-like conversion upon CTCF depletion. Transcriptional activation of the ZSCAN4 cluster is necessary for successful 2C-like reprogramming. Auxin-inducible degron CTCF depletion in ESCs, flow cytometry, RNA-seq, CTCF ChIP-seq Nature communications Medium 34381034
2022 The NURF chromatin remodeling complex (via its specific subunit BPTF) creates local chromatin accessibility around CTCF sites by positioning the SNF2H ATPase, enabling CTCF binding. At a subset of sites where chromatin accessibility decreases without NURF/BPTF, CTCF binding can persist but cohesin occupancy is reduced, resulting in decreased insulation — demonstrating that CTCF binding can be experimentally separated from its insulator function in nuclear organization. Isogenic mouse stem cell panel with individual ISWI subunit knockouts (CRISPR), ATAC-seq, CTCF and cohesin ChIP-seq, Hi-C Nature genetics High 38816647
2021 CTCF depletion markedly rewires genome-wide chromatin accessibility. Increased accessible chromatin regions appear adjacent to CTCF-binding sites at promoters and insulator sites, associated with enhanced transcription of nearby genes. Combinatorial multi-omics analysis identified 40 CTCF co-regulatory partners; many altered downstream gene expression without changing their own expression upon CTCF loss. Auxin-inducible degron CTCF depletion with ATAC-seq, RNA-seq, WGBS, Hi-C, proteomics/phosphoproteomics, CRISPR dropout screens Genome biology Medium 34429148
2021 CTCF directly suppresses transcription of POLD1 (DNA polymerase δ catalytic subunit) by binding to its promoter. CTCF binding to the POLD1 promoter decreases with aging, and shRNA knockdown of CTCF reduces POLD1 expression, accelerating cell senescence. Overexpression of CTCF maintains POLD1 expression and slows senescence, establishing CTCF as a positive transcriptional regulator of POLD1. ChIP (CTCF–POLD1 promoter binding), shRNA knockdown, overexpression, senescence assays Frontiers in cell and developmental biology Low 33692996
2021 CTCF is required for correct fate specification and migration of MGE-derived cortical interneurons (CINs). Conditional Ctcf ablation in the medial ganglionic eminence leads to delayed tangential migration, abnormal distribution of CINs, marked reduction of parvalbumin- and somatostatin-expressing CINs, and increased cells expressing Lhx8 (basal forebrain marker). Ctcf-null MGE cells transplanted into wild-type cortex recapitulate these defects, and re-expression of LHX6 rescues lamination defects, indicating CTCF regulates the Lhx6/Lhx8 dichotomy for correct CIN specification. Conditional Ctcf knockout in MGE (mouse), transplantation assay, LHX6 rescue by overexpression, immunohistochemistry/in situ hybridization The Journal of neuroscience High 30377227
2022 Live-cell imaging at high spatial and temporal resolution showed that chromatin interactions within TADs are transient and occur frequently during the cell cycle. Interactions become more frequent and longer-lived with convergent CTCF sites, suppressing variability in chromosome folding. Physical models supported CTCF-anchored loops lasting ~10 min, consistent with cohesin stabilizing dynamic chromosome structures. High-resolution live-cell imaging of chromosomal loci, polymer physics modeling Nature genetics High 36471076
2020 The N-terminus of CTCF interacts with cohesin, explaining the requirement for convergent CTCF binding sites in loop formation. CTCFL (BORIS) and CTCF have distinct binding characteristics: phenotypically distinct sites show differences in motifs, promoter/intronic targeting, and chromatin folding. The N, C, and zinc finger terminal domains of CTCF and CTCFL play unique roles in targeting each paralog to distinct binding sites to regulate transcription, chromatin looping, and insulation. Inducible complementation system expressing CTCF, CTCFL, and CTCF-CTCFL chimeras; ChIP-seq, Hi-C, RNA-seq Genome biology Medium 32393311
2021 G-quadruplex (G4) structures bind CTCF protein directly in vitro with Kd values similar to control duplexes, while i-motifs show no affinity for CTCF. G4-stabilizing ligands enhance CTCF occupancy at a G4-prone STAT3 gene site by ChIP-qPCR. HMGN3 (a high mobility group protein that recognizes G4s) co-localizes with G4s at CTCF sites and contributes to CTCF–G4 association. In vitro binding assays, ChIP-qPCR with G4-stabilizing ligands, bioinformatic co-localization analysis International journal of molecular sciences Medium 34209337
2022 TRF2 physically interacts with CTCF, and CTCF drives proper positioning of TRF2 on a binding site upstream of the miR-193b-3p host-gene. TRF2 binding at this CTCF-positioned site is necessary for promoting miR-193b-3p expression, which inhibits SUV39H1 translation and promotes colorectal cancer cell proliferation. Co-immunoprecipitation for TRF2–CTCF interaction, ChIP for TRF2 positioning, CTCF knockdown, miRNA expression assays Cancer letters Medium 35240232
2019 Absolute quantification by mass spectrometry, fluorescence-correlation spectroscopy, and FRAP in HeLa cells revealed ~250,000 nuclear cohesin complexes and ~160,000 chromatin-bound cohesin in G1-phase, with CTCF at a defined stoichiometry. Comparison with ChIP-seq data implies some genomic CTCF and cohesin enrichment sites are unoccupied in single cells at any one time, with implications for how loops are formed stochastically. Mass spectrometry, fluorescence-correlation spectroscopy (FCS), FRAP, compared with ChIP-seq occupancy data eLife High 31204999
2023 CTCF cooperates with lineage-specific pioneer transcription factors (MyoD, FOXA, PU.1) to control cell identity. Pioneer TFs facilitate lineage-specific CTCF occupancy by opening chromatin (1D level). CTCF and pioneer TFs form regulatory hubs governing cell identity gene expression (3D level). Validated in MyoD-null mice, CTCF knockout mice, and CRISPR editing during myogenic differentiation. Integrative ChIP-seq/ATAC-seq analysis, MyoD-null and CTCF-KO mouse models, CRISPR editing in myogenic differentiation Cell reports Medium 37851578
2024 Coordinate disruption of four CTCF motifs at a TAD boundary fuses adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes robust FGF3 induction. High-resolution micro-C maps revealed specific contacts between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scale with FGF3 induction, establishing that modest changes in contact frequency cause strong changes in gene expression, consistent with a causal relationship between CTCF-mediated boundary insulation and enhancer–oncogene regulation. CRISPR deletion of four CTCF motifs, micro-C for high-resolution chromatin contacts, RNA-seq, comparison with GIST patient data Molecular cell High 38452764
2023 During formation of new CTCF loops in pancreatic differentiation, recruitment of CTCF to new anchor sites involves demethylation of H3K9me3 to H3K9me2, DNA demethylation, recruitment of pioneer factors, and positioning of flanking nucleosomes. Pre-existing CTCF sites that are not initially involved in looping become functional loop anchors via establishment of new cohesin-loading sites containing NIPBL and YY1 between anchors. New CTCF loop formation leads to strengthened enhancer–promoter interactions and increased transcription. ChIP-seq (CTCF, cohesin, histone marks), ATAC-seq, Hi-C, DNA methylation profiling during hESC-to-pancreatic islet differentiation Nature communications Medium 37813869
2021 Boundary-associated RNAs (transcribed from active TAD enhancers) facilitate CTCF recruitment and clustering at TAD borders, enhancing insulation. Knockdown of boundary-associated RNAs causes loss of boundary insulation function. CTCF site deletions and enhancer deletions (but not promoter CRISPRi) reduce boundary RNA transcription and CTCF enrichment, defining a regulatory axis: active TAD enhancers → boundary RNA → CTCF clustering → insulation. CTCF site deletions, enhancer deletions, CRISPRi, RNA knockdown, CTCF ChIP-seq, Hi-C, 4C-seq Genome research Medium 36650052
2022 MYC protein directly interacts with CTCF and colocalizes at a subset of genomic sites in prostate cancer cells, enhancing CTCF occupancy at these sites. MYC activation potentiates CTCF-mediated chromatin looping and disrupts enhancer–promoter looping at neuroendocrine lineage plasticity genes, defining MYC as a CTCF co-factor in 3D genome organization. Co-immunoprecipitation for MYC-CTCF interaction, HiChIP (H3K27ac, AR, CTCF), CRISPR deletion of CTCF site upstream of MYC, ChIP-seq Nature communications Medium 36997534
2021 CTCF combined action with its paralog BORIS is required for spermatogenesis. In compound mutant mice (Ctcf+/-Boris-/-), chromatin binding of CTCF is preferentially lost from CTCF-BORIS heterodimeric sites. Loss leads to reduced expression of spermatogenesis genes and inappropriate gain of developmentally toxic genes, resulting in male sterility. BORIS heterodimerizes with CTCF specifically at these sites. Compound Ctcf/Boris mouse mutants, CTCF ChIP-seq, RNA-seq, fertility assays Nature communications High 34158481
2021 CTCF binding to the SMARCA5 (ISWI ATPase) locus is facilitated by SMARCA5 itself, and SMARCA5 supports CTCF's enhancer-blocking function at the H19/Igf2 imprinting control region. Both CTCF and SMARCA5 are co-recruited to the SPI1 gene regulatory regions during myeloid differentiation; DNA methylation at the SPI1 locus in AML blasts blocks CTCF binding and subsequent SMARCA5 recruitment. ChIP for CTCF and SMARCA5, insulator/enhancer-blocking assay, AZA-mediated DNA demethylation, knockdown PloS one Medium 24498324
2022 Cohesin complexes at CTCF sites are released from DNA and loops lost when the cohesin ring is opened by RAD21 cleavage, while cohesin-dependent loops within chromatin domains not anchored at CTCF pairs are more resistant to RAD21 cleavage. This indicates cohesin mediates loops through different mechanisms depending on whether they are CTCF-anchored, suggesting structural changes as cohesin dynamically extrudes and encounters CTCF sites. Engineered cleavable RAD21 in isolated nuclei, Hi-C, cohesin ChIP-seq Nature cell biology High 36202971

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2017 Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell 1300 28525758
2009 CTCF: master weaver of the genome. Cell 1267 19563753
2014 CTCF: an architectural protein bridging genome topology and function. Nature reviews. Genetics 795 24614316
2015 CTCF Binding Polarity Determines Chromatin Looping. Molecular cell 488 26527277
2001 CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends in genetics : TIG 480 11525835
2017 CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife 476 28467304
2022 Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science (New York, N.Y.) 398 35420890
2016 CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation. Annual review of genomics and human genetics 388 27089971
2013 CTCF and cohesin: linking gene regulatory elements with their targets. Cell 282 23498937
2019 RNA Interactions Are Essential for CTCF-Mediated Genome Organization. Molecular cell 226 31522988
2016 CTCF: making the right connections. Genes & development 216 27083996
2004 Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation. Nature genetics 216 15361875
2022 Cohesin and CTCF control the dynamics of chromosome folding. Nature genetics 193 36471076
2013 CTCF: the protein, the binding partners, the binding sites and their chromatin loops. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 178 23650640
2020 CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention. Proceedings of the National Academy of Sciences of the United States of America 162 31937660
2014 CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer. Cell reports 151 24794443
2008 Genetics and epigenetics of the multifunctional protein CTCF. Current topics in developmental biology 141 17950379
2023 CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion. Nature 129 37076620
2012 CTCF: insights into insulator function during development. Development (Cambridge, England) 123 22354838
2009 CTCF and its protein partners: divide and rule? Journal of cell science 119 19386894
2018 Developing in 3D: the role of CTCF in cell differentiation. Development (Cambridge, England) 113 29567640
2019 Absolute quantification of cohesin, CTCF and their regulators in human cells. eLife 96 31204999
2020 Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. Genome biology 89 32933554
2023 Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nature genetics 84 36717694
2023 CTCF and R-loops are boundaries of cohesin-mediated DNA looping. Molecular cell 80 37536339
2023 G-quadruplexes associated with R-loops promote CTCF binding. Molecular cell 75 37552993
2021 Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops. Cell 75 34856126
2019 CTCF: a Swiss-army knife for genome organization and transcription regulation. Essays in biochemistry 75 30940740
2020 DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex. Molecular cell 73 32333838
2022 CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nature genetics 71 35145304
2017 CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals. Cell systems 70 29199022
2019 DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome research 67 30948436
2019 CTCF confers local nucleosome resiliency after DNA replication and during mitosis. eLife 66 31599722
2020 CTCF and CTCFL in cancer. Current opinion in genetics & development 64 32334335
2021 CTCF and transcription influence chromatin structure re-configuration after mitosis. Nature communications 61 34453048
2011 CTCF function is modulated by neighboring DNA binding factors. Biochemistry and cell biology = Biochimie et biologie cellulaire 55 21895576
2021 CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic acids research 53 34181707
2022 CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. Nature cell biology 51 36202971
2019 An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis. Nature communications 51 30948729
2021 CTCF is a barrier for 2C-like reprogramming. Nature communications 49 34381034
2021 Acute depletion of CTCF rewires genome-wide chromatin accessibility. Genome biology 49 34429148
2015 Genetic Tailors: CTCF and Cohesin Shape the Genome During Evolution. Trends in genetics : TIG 49 26439501
2020 Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation. Genome biology 48 32393311
2018 Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features. Nature communications 47 30310060
2013 CTCF and BORIS in genome regulation and cancer. Current opinion in genetics & development 46 24657531
2012 The tumor suppressor role of CTCF. Journal of cellular physiology 45 21465478
2018 Predicting CTCF-mediated chromatin loops using CTCF-MP. Bioinformatics (Oxford, England) 44 29949986
2016 CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions. Nucleic acids research 44 27638884
2005 Poly(ADP-ribosyl)ation and epigenetics. Is CTCF PARt of the plot? Cell cycle (Georgetown, Tex.) 43 15655363
2015 Patterns of CTCF and ZFHX3 Mutation and Associated Outcomes in Endometrial Cancer. Journal of the National Cancer Institute 42 26330387
2014 The role of CCCTC-binding factor (CTCF) in genomic imprinting, development, and reproduction. Biology of reproduction 42 25297545
2024 The impact of DNA methylation on CTCF-mediated 3D genome organization. Nature structural & molecular biology 40 38499830
2021 Loop competition and extrusion model predicts CTCF interaction specificity. Nature communications 39 33594051
2019 NPM1c impedes CTCF functions through cytoplasmic mislocalization in acute myeloid leukemia. Leukemia 38 31831844
2012 The role of CTCF in regulating V(D)J recombination. Current opinion in immunology 38 22424610
2020 CTCF loss mediates unique DNA hypermethylation landscapes in human cancers. Clinical epigenetics 37 32503656
2008 Cohesin and CTCF: cooperating to control chromosome conformation? BioEssays : news and reviews in molecular, cellular and developmental biology 37 18623068
2018 CTCF maintains regulatory homeostasis of cancer pathways. Genome biology 36 30086769
2023 Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries. Genome research 35 36650052
2013 Cohesin and CTCF differentially regulate spatiotemporal runx1 expression during zebrafish development. Biochimica et biophysica acta 34 24321385
2023 MYC reshapes CTCF-mediated chromatin architecture in prostate cancer. Nature communications 33 36997534
2018 Dopamine Triggers CTCF-Dependent Morphological and Genomic Remodeling of Astrocytes. The Journal of neuroscience : the official journal of the Society for Neuroscience 32 29712779
2023 Structures of CTCF-DNA complexes including all 11 zinc fingers. Nucleic acids research 30 37439339
2020 LATS kinase-mediated CTCF phosphorylation and selective loss of genomic binding. Science advances 30 32128389
2014 Epigenetic control of SPI1 gene by CTCF and ISWI ATPase SMARCA5. PloS one 30 24498324
2018 Roles of CTCF in conformation and functions of chromosome. Seminars in cell & developmental biology 29 30031212
2024 Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation. Molecular cell 27 38452764
2023 CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors. Cell reports 27 37851578
2015 CTCF negatively regulates HOXA10 expression in breast cancer cells. Biochemical and biophysical research communications 27 26478432
2018 Role of CTCF in DNA damage response. Mutation research. Reviews in mutation research 26 31395350
2017 The connection between BRG1, CTCF and topoisomerases at TAD boundaries. Nucleus (Austin, Tex.) 26 28060558
2022 CTCF: A misguided jack-of-all-trades in cancer cells. Computational and structural biotechnology journal 25 35685367
2022 Characterization and perturbation of CTCF-mediated chromatin interactions for enhancing myogenic transdifferentiation. Cell reports 25 35977522
2021 Cooperation of ATF4 and CTCF promotes adipogenesis through transcriptional regulation. Cell biology and toxicology 25 33950334
2022 CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. Genome biology 24 36050765
2021 DNA G-Quadruplexes Contribute to CTCF Recruitment. International journal of molecular sciences 24 34209337
2018 CTCF Governs the Identity and Migration of MGE-Derived Cortical Interneurons. The Journal of neuroscience : the official journal of the Society for Neuroscience 24 30377227
2017 CTCF deletion syndrome: clinical features and epigenetic delineation. Journal of medical genetics 24 28848059
2022 CTCF blocks antisense transcription initiation at divergent promoters. Nature structural & molecular biology 23 36369346
2021 Super-Enhancers and CTCF in Early Embryonic Cell Fate Decisions. Frontiers in cell and developmental biology 23 33842482
2021 The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis. Nature communications 23 34158481
2012 Cohesin, CTCF and lymphocyte antigen receptor locus rearrangement. Trends in immunology 23 22440186
2024 Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF. Nature genetics 22 38816647
2022 CTCF and Its Partners: Shaper of 3D Genome during Development. Genes 22 36011294
2021 Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress. PLoS genetics 22 33411704
2018 A tour of 3D genome with a focus on CTCF. Seminars in cell & developmental biology 22 30031214
2020 CTCF-mediated genome organization and leukemogenesis. Leukemia 21 32518417
2020 Many facades of CTCF unified by its coding for three-dimensional genome architecture. Journal of genetics and genomics = Yi chuan xue bao 21 33187878
2018 CTCF Expression is Essential for Somatic Cell Viability and Protection Against Cancer. International journal of molecular sciences 21 30513694
2014 Vigilin interacts with CCCTC-binding factor (CTCF) and is involved in CTCF-dependent regulation of the imprinted genes Igf2 and H19. The FEBS journal 21 24725430
2023 CTCF and Its Multi-Partner Network for Chromatin Regulation. Cells 20 37408191
2021 CTCF Mediates Replicative Senescence Through POLD1. Frontiers in cell and developmental biology 20 33692996
2021 Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer. Cellular and molecular life sciences : CMLS 20 34657170
2024 Hypoxia-induced CTCF promotes EMT in breast cancer. Cell reports 19 38900639
2023 CTCF mediates CD8+ effector differentiation through dynamic redistribution and genomic reorganization. The Journal of experimental medicine 19 36752796
2023 Regulation of CTCF loop formation during pancreatic cell differentiation. Nature communications 19 37813869
2022 TRF2 cooperates with CTCF for controlling the oncomiR-193b-3p in colorectal cancer. Cancer letters 19 35240232
2015 CTCF regulates NELF, DSIF and P-TEFb recruitment during transcription. Transcription 19 26399478
2022 CTCF: an R/bioconductor data package of human and mouse CTCF binding sites. Bioinformatics advances 18 36699364
2017 CTCF, Cohesin, and Chromatin in Human Cancer. Genomics & informatics 17 29307136

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