{"gene":"LSM11","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2003,"finding":"Lsm11 is a novel Sm-like protein that replaces SmD2 in the U7 snRNP Sm ring. Its long N-terminal domain mediates an important step in histone mRNA 3'-end cleavage, while its C-terminal Sm motifs (interrupted by an unusually long spacer) are sufficient for assembly with U7 snRNA. Assembly of the U7-specific Sm core depends on the noncanonical Sm-binding site of U7 snRNA and is facilitated by a specialized SMN complex containing Lsm10 and Lsm11 but lacking SmD1/D2.","method":"In vitro assembly assays, immunoprecipitation, GST pulldown, in vitro processing assays, domain deletion/truncation analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro reconstitution of assembly, multiple domain truncations, functional processing assays, and reciprocal IPs; foundational study replicated by multiple subsequent labs","pmids":["12975319"],"is_preprint":false},{"year":2003,"finding":"Drosophila Lsm11 (dLsm11) associates with dLsm10, SmB (but not SmD1/D2), and the Drosophila U7 snRNA, and indirectly with histone H3 pre-mRNA; dLsm10 and dLsm11 can assemble into U7 snRNPs in mammalian cells, demonstrating evolutionary conservation of the unique U7 snRNP composition.","method":"Immunoprecipitation in Drosophila S2 cells, cross-species complementation assay","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP in S2 cells and cross-species assembly assay, single lab","pmids":["14624008"],"is_preprint":false},{"year":2005,"finding":"Lsm11 undergoes two distinct interactions with ZFP100: one between the Lsm11 N-terminus and the zinc finger repeats of ZFP100, and a second between the N-terminus of ZFP100 and the Sm domain of Lsm11. The second interaction is sufficient for specific recognition of U7 snRNP by ZFP100 in cell extracts. Clustered point mutations in three conserved regions of the Lsm11 N-terminus impair histone RNA processing independently of ZFP100 binding, indicating additional roles (e.g., contacting the pre-mRNA or other factors).","method":"GST pulldown (in vitro and in cell extracts), scanning mutagenesis, in vitro processing assays","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding assays with mutagenesis and functional processing readout, single lab","pmids":["15824063"],"is_preprint":false},{"year":2005,"finding":"Lsm10 and Lsm11 associate with the pICln subunit of the PRMT5 complex in vitro and in vivo without receiving symmetrical dimethylarginine (sDMA) modifications, implicating the PRMT5 complex in an early stage of U7 snRNP assembly independent of methylation. Binding of Lsm10 and Lsm11 to SMN is independent of methylation, and two separate binding sites exist in SMN: one recognizing Sm domains and one recognizing sDMA-modified RG-tails.","method":"Co-immunoprecipitation, GST pulldown, in vitro binding assays, methylation assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP in cells plus in vitro pulldown, single lab with multiple orthogonal methods","pmids":["16087681"],"is_preprint":false},{"year":2006,"finding":"ZFP100 zinc fingers 5–10 are required for binding to a 20-amino-acid region of Lsm11, and the domain sufficient for Cajal body localization and Lsm11 binding is also sufficient to stimulate histone pre-mRNA processing in vivo, linking the ZFP100–Lsm11 interaction to processing activity.","method":"Co-immunoprecipitation, domain truncation, in vivo reporter assay, photobleaching (FRAP)","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, functional reporter, and domain mapping in a single lab","pmids":["16714279"],"is_preprint":false},{"year":2007,"finding":"Lsm11 localizes to the histone locus body (HLB) in Drosophila embryos; using anti-Lsm11 antibodies, the HLB is shown to form at nuclear cycle 11 coincident with zygotic histone transcription. Lsm11 foci are present even in histone locus deletion embryos, indicating HLB assembly is not strictly dependent on the histone locus itself.","method":"Immunofluorescence, confocal microscopy, genetic ablation of histone locus in embryos","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by antibody staining with genetic controls, single lab","pmids":["17442888"],"is_preprint":false},{"year":2009,"finding":"FLASH directly interacts with Lsm11 in vitro and in vivo (by yeast two-hybrid and immunoprecipitation), stimulates 3'-end processing of histone pre-mRNA in mammalian nuclear extracts, and is essential for U7-dependent processing in both vertebrates (human) and invertebrates (Drosophila), with FLASH depletion leading to polyadenylation of histone mRNAs.","method":"Yeast two-hybrid, GST pulldown (in vitro), co-immunoprecipitation (in vivo), in vitro processing assay (mammalian nuclear extracts), RNAi knockdown in Drosophila cells","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (Y2H, in vitro pulldown, reciprocal Co-IP, in vitro processing, in vivo RNAi) across two organisms; replicated by subsequent studies","pmids":["19854135"],"is_preprint":false},{"year":2009,"finding":"Three components of the U7-specific Sm ring—SmB, SmD3, and Lsm10—contact the region between the cleavage site and U7-binding site in histone pre-mRNA and likely function as a molecular ruler determining the cleavage site. Lsm11 and SmB were identified as stable components of the 3'-end processing complex assembled on histone pre-mRNA.","method":"Biotin-affinity pulldown of processing complex from nuclear extracts, UV cross-linking, mass spectrometry identification","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — affinity purification with UV cross-linking and mass spectrometry, single lab","pmids":["19470752"],"is_preprint":false},{"year":2009,"finding":"Mutations in Drosophila Lsm11 disrupt histone pre-mRNA processing (causing polyadenylated histone mRNA). Lsm10 protein fails to accumulate in Lsm11 mutants, suggesting Lsm10–Lsm11 dimers are precursors for U7 snRNP assembly. Lsm11 is required for U7 snRNA localization to the histone locus body, even though U7 snRNA can still assemble into a trimethylguanosine-capped particle in the absence of Lsm11. Lsm10 and Lsm11 mutants, unlike U7 snRNA null mutants, are lethal, indicating an essential Lsm10/Lsm11 function beyond histone pre-mRNA processing.","method":"Drosophila genetics (null mutants), RT-PCR, immunofluorescence, anti-TMG immunoprecipitation","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function with molecular phenotyping, localization studies, and biochemical fractionation; multiple orthogonal methods","pmids":["19620235"],"is_preprint":false},{"year":2010,"finding":"CF Im68, a cleavage/polyadenylation factor, associates with highly purified U7 snRNP and this interaction depends on the N-terminus of Lsm11. Both depletion and overexpression of CF Im68 reduce histone RNA processing efficiency in vivo. The small CF Im subunit CF Im25 does not participate in histone RNA processing.","method":"Biochemical purification of U7 snRNP, immunoprecipitation, siRNA knockdown, in vitro processing assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — purification plus functional in vitro and in vivo assays, single lab","pmids":["20634199"],"is_preprint":false},{"year":2011,"finding":"Amino acids 105–154 of Drosophila FLASH bind to amino acids 1–78 of dLsm11 (N-terminal domain). A two-amino-acid mutation in dLsm11 that abolishes dFLASH binding, without affecting U7 snRNP localization to the HLB, fails to rescue lethality or processing defects caused by Lsm11 null mutation, demonstrating that the FLASH–Lsm11 protein–protein interaction is essential for histone pre-mRNA processing in vivo.","method":"Drosophila genetic rescue assay (null mutation complementation), yeast two-hybrid, co-immunoprecipitation, site-directed mutagenesis, immunofluorescence","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — genetic rescue with point mutations plus binding assays and localization; multiple orthogonal methods defining interaction domain and in vivo requirement","pmids":["21525146"],"is_preprint":false},{"year":2011,"finding":"Scanning mutagenesis identified critical residues in human Lsm11 that mediate its interaction with FLASH. Mutations in FLASH between residues 50–99 that do not affect Lsm11 binding convert FLASH into an inhibitory dominant negative, suggesting this FLASH region plus Lsm11 recruits an additional unknown processing factor. After endonucleolytic cleavage, the 5'→3' exonuclease activity of CPSF73 on the downstream cleavage product depends on Lsm11 but not on FLASH, indicating FLASH is dispensable for activating the exonuclease mode.","method":"Scanning mutagenesis, GST pulldown, in vitro processing assay with mammalian nuclear extracts, antibody inhibition","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro functional assay combined with systematic mutagenesis, single lab","pmids":["21245389"],"is_preprint":false},{"year":2012,"finding":"The N-terminal regions of FLASH and Lsm11 form a platform that recruits a specific set of polyadenylation factors—symplekin, CstF64, and all CPSF subunits including the CPSF73 endonuclease—to the U7 snRNP. Point mutations in FLASH that abolish processing also inhibit this interaction. The same polyadenylation factors associate with endogenous U7 snRNP and are recruited to histone pre-mRNA in a U7-dependent manner.","method":"Co-immunoprecipitation (reciprocal), in vitro binding assays, point mutagenesis, mass spectrometry, histone pre-mRNA pull-down","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vitro binding with mutagenesis, mass spectrometry confirmation of endogenous complex; replicated in Drosophila by a subsequent independent study","pmids":["23071092"],"is_preprint":false},{"year":2013,"finding":"The Drosophila U7 snRNP contains FLASH and at least six polyadenylation factors (symplekin, CPSF73, CPSF100, CPSF160, WDR33, CstF64) as stable stoichiometric components, and this composite particle is recruited to histone pre-mRNA for processing. A motif in Drosophila FLASH is essential for recruiting the polyadenylation complex to U7 snRNP via Lsm11.","method":"Biochemical purification from Drosophila nuclear extracts, mass spectrometry, RNAi knockdown, in vitro processing assay","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — biochemical purification with MS identification, functional RNAi, and in vitro processing; independent replication of mammalian findings in Drosophila","pmids":["24145821"],"is_preprint":false},{"year":2017,"finding":"SLBP stabilizes U7 snRNP binding to histone pre-mRNA via two regions (helix B of its RNA-binding domain and C-terminal region), and this stabilization requires FLASH but not the downstream polyadenylation factors, assigning FLASH a second role: cooperating with SLBP to recruit U7 snRNP to histone pre-mRNA, distinct from its role in forming the polyadenylation factor docking platform with Lsm11.","method":"EMSA (gel shift), in vitro processing assay, domain truncation of SLBP/FLASH, UV cross-linking","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding and processing assays with domain truncations, single lab","pmids":["28289156"],"is_preprint":false},{"year":2017,"finding":"Crystal structures of the FLASH N-terminal domain reveal it forms a coiled-coil dimer. Solution light scattering, analytical ultracentrifugation, and crosslinking show the FLASH NTD–Lsm11 NTD complex is a 2:1 heterotrimer (two FLASH NTD molecules per one Lsm11 NTD).","method":"X-ray crystallography, multi-angle light scattering, analytical ultracentrifugation, chemical crosslinking","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus multiple orthogonal biophysical methods to establish stoichiometry; single lab but rigorous","pmids":["29020104"],"is_preprint":false},{"year":2019,"finding":"ALYREF physically interacts with Lsm11 (U7-snRNP-specific component) and promotes histone pre-mRNA 3'-end processing by facilitating U7-snRNP recruitment to histone pre-mRNA. ALYREF also enhances nuclear export of processed histone mRNAs as part of the TREX complex.","method":"Co-immunoprecipitation, RNA-immunoprecipitation, siRNA knockdown with processing and export assays","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and functional knockdown assays, single lab","pmids":["30858280"],"is_preprint":false},{"year":2020,"finding":"Biallelic mutations in LSM11 (encoding a component of the U7 snRNP histone pre-mRNA processing complex) cause misprocessing of canonical histone transcripts, disturb linker histone stoichiometry, alter nuclear cGAS distribution, and enhance cGAS-STING-mediated type I interferon signaling, establishing LSM11 as an Aicardi-Goutières syndrome gene. Chromatin lacking linker histone stimulates cGAMP production more efficiently in vitro, linking histone processing defects to innate immune activation.","method":"Patient-derived fibroblast studies, RT-PCR (histone mRNA processing), cGAS localization (immunofluorescence), cGAS in vitro cGAMP synthesis assay with reconstituted chromatin, interferon signaling assays","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods in patient cells plus in vitro mechanistic reconstitution; published in a high-scrutiny journal","pmids":["33230297"],"is_preprint":false},{"year":2022,"finding":"SMN-mediated assembly of U7 snRNP (requiring Lsm10 and Lsm11) is necessary for neuromuscular junction (NMJ) integrity; co-expression of Lsm10 and Lsm11 selectively enhances U7 snRNP assembly, corrects histone mRNA processing defects, and rescues NMJ denervation, synaptic transmission defects, and skeletal muscle atrophy in SMA mice. U7 snRNP dysfunction also drives selective loss of the synaptic organizer Agrin at NMJs in vulnerable muscles.","method":"Mouse SMA model (in vivo), AAV-mediated co-expression of Lsm10/Lsm11, RT-PCR (histone mRNA processing), electrophysiology (NMJ transmission), immunofluorescence (NMJ morphology), Western blot (Agrin levels)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo rescue with Lsm10/Lsm11, multiple orthogonal functional readouts, mouse model with rigorous controls","pmids":["36130491"],"is_preprint":false},{"year":2023,"finding":"A heterodimer of Lsm10 and Lsm11 tightly interacts with the PRMT5/MEP50/pICln methylosome. Cryo-EM structural studies and biochemical assays show the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the N-terminal region of Lsm11. PRMT5 also methylates an N-terminal arginine in SmE specifically in the U7 context (SmE is not methylated during spliceosomal Sm ring biogenesis).","method":"Cryo-EM structure determination, in vitro methylation assay, co-immunoprecipitation, biochemical binding assays","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure plus in vitro enzymatic assay and biochemical binding; single lab but multiple orthogonal methods","pmids":["37562960"],"is_preprint":false},{"year":2023,"finding":"A SUMO-interacting motif (SIM) in the N-terminus of Lsm11 is required for efficient formation of U7 snRNP; in SUMO2 knockout cells, U7 snRNP levels are reduced and histone pre-mRNA 3'-end cleavage is defective with increased histone mRNA polyadenylation. Overexpression of Lsm11 and U7 snRNA rescues U7 snRNP levels and processing defects in SUMO2 KO cells.","method":"SUMO2 knockout cell line, rescue by Lsm11/U7 snRNA overexpression, RT-PCR (histone mRNA processing), immunofluorescence (HLB dynamics), SIM deletion mutagenesis","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO cell line with mutagenesis and rescue, multiple functional readouts; single lab","pmids":["40639911"],"is_preprint":false},{"year":2026,"finding":"A conserved N-terminal helix of Lsm11 contacts the metallo-β-lactamase domain of the CPSF73 endonuclease within U7 snRNP; mutating or deleting this helix substantially reduces cleavage activity toward histone pre-mRNA. Cryo-EM of reconstituted wild-type U7 snRNP on a noncleavable pre-mRNA shows CPSF73 can adopt an open, active conformation independent of RNA binding at its active site. The CstF77 C-terminus contacts the CPSF100 subunit at a newly identified binding site that modestly contributes to cleavage activity.","method":"Cryo-EM structure determination, site-directed mutagenesis (helix deletion/point mutants), in vitro cleavage assay, reconstitution of U7 snRNP with pre-mRNA","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure plus mutagenesis and in vitro activity reconstitution; single lab but multiple orthogonal methods","pmids":["41495886"],"is_preprint":false},{"year":2016,"finding":"Hydrogen/deuterium exchange mass spectrometry shows the FLASH-interacting domain in Lsm11 is highly dynamic, while a downstream region required for recruiting the histone cleavage complex (HCC) folds into a stable structure. In vitro binding assays reveal Lsm11 also contacts the C-terminal SANT/Myb-like domain of FLASH (the same region that binds NPAT), and this binding partially relaxes (destabilizes) that domain, suggesting competition between Lsm11 and NPAT for FLASH that may regulate histone gene expression.","method":"Hydrogen/deuterium exchange mass spectrometry, in vitro GST pulldown binding assays","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — HDX-MS plus in vitro binding assays; single lab, two orthogonal methods","pmids":["26860583"],"is_preprint":false}],"current_model":"LSM11 is a U7 snRNP-specific Sm-like protein that replaces SmD2 in the heptameric Sm ring; its N-terminal extension (stabilized by a conserved helix that contacts CPSF73, and methylated by PRMT5 via a PRMT5-Lsm10/Lsm11 interaction) docks FLASH in a 2:1 FLASH:Lsm11 heterotrimer, which together recruit the CPSF73 endonuclease and associated polyadenylation factors (symplekin, CstF64, CPSF subunits) to catalyze endonucleolytic 3'-end cleavage of replication-dependent histone pre-mRNAs; loss of functional Lsm11 causes histone mRNA misprocessing, disrupts linker histone stoichiometry, activates cGAS-STING-mediated type I interferon signaling (causing Aicardi-Goutières syndrome), and impairs neuromuscular junction integrity in SMA models."},"narrative":{"mechanistic_narrative":"LSM11 is a U7 snRNP-specific Sm-like protein that constitutes the catalytic engine for endonucleolytic 3'-end cleavage of replication-dependent histone pre-mRNAs [PMID:12975319, PMID:19854135]. It replaces SmD2 in the heptameric Sm ring, assembling with Lsm10 onto the noncanonical Sm-binding site of U7 snRNA via a specialized SMN complex; its C-terminal Sm motifs (split by a long spacer) drive ring assembly while its extended N-terminal domain carries the processing function [PMID:12975319]. This N-terminal domain docks FLASH, forming a 2:1 FLASH:Lsm11 heterotrimer whose paired N-terminal regions build a platform that recruits the cleavage/polyadenylation machinery—symplekin, CstF64, and the CPSF subunits including the CPSF73 endonuclease—to the U7 snRNP [PMID:23071092, PMID:29020104]. A conserved N-terminal helix of Lsm11 directly contacts the metallo-β-lactamase domain of CPSF73 and is required for efficient cleavage, and CPSF73 exonuclease activity on the downstream product depends on Lsm11 [PMID:21245389, PMID:41495886]. Assembly and activity of this machinery are governed by additional layers: PRMT5 methylates two arginines in the Lsm11 N-terminus and tethers the Lsm10/Lsm11 heterodimer to the methylosome [PMID:37562960], a SUMO-interacting motif promotes efficient U7 snRNP formation [PMID:40639911], and the particle is recruited to histone pre-mRNA cooperatively with SLBP, FLASH, and ALYREF [PMID:28289156, PMID:30858280]. Biallelic LSM11 mutations cause Aicardi-Goutières syndrome by misprocessing histone transcripts, disturbing linker histone stoichiometry, and activating cGAS-STING type I interferon signaling [PMID:33230297].","teleology":[{"year":2003,"claim":"Established that LSM11 is a U7 snRNP-specific Sm-like protein with a functional division of labor between its domains, answering what distinguishes the histone-processing snRNP from spliceosomal snRNPs.","evidence":"In vitro assembly, IP, GST pulldown, and processing assays with domain truncations; cross-species Co-IP in Drosophila S2 cells","pmids":["12975319","14624008"],"confidence":"High","gaps":["Mechanism of how the N-terminal domain drives cleavage not defined at this stage","Direct cleavage factors recruited by Lsm11 not yet identified"]},{"year":2005,"claim":"Mapped Lsm11 N-terminal interactions with ZFP100 and the PRMT5/pICln complex, beginning to define how the U7 snRNP recognizes processing partners and is routed through assembly.","evidence":"GST pulldown, scanning mutagenesis, in vitro processing, and Co-IP/methylation assays","pmids":["15824063","16087681","16714279"],"confidence":"Medium","gaps":["ZFP100 interaction later superseded as the key processing tether by FLASH","Functional consequence of PRMT5 association on Lsm11 not resolved here","Additional N-terminal contacts inferred but partners unidentified"]},{"year":2007,"claim":"Localized Lsm11 to the histone locus body, linking the protein to the nuclear compartment where histone gene expression is organized.","evidence":"Immunofluorescence and confocal microscopy in Drosophila embryos with histone locus genetic ablation","pmids":["17442888"],"confidence":"Medium","gaps":["What nucleates HLB assembly independent of the histone locus unknown","Role of Lsm11 in HLB formation vs. recruitment not separated"]},{"year":2009,"claim":"Identified FLASH as the essential Lsm11-binding factor for processing and showed Lsm11 is required in vivo for U7 snRNP function and viability beyond histone processing.","evidence":"Y2H, GST pulldown, reciprocal Co-IP, in vitro processing, RNAi, and Drosophila null mutant genetics with molecular phenotyping","pmids":["19854135","19620235","19470752"],"confidence":"High","gaps":["How FLASH-Lsm11 enables cleavage not yet mechanistic","Identity of the essential non-processing Lsm10/Lsm11 function undefined"]},{"year":2011,"claim":"Defined the FLASH-Lsm11 interaction at residue resolution and proved by genetic rescue that this protein-protein contact is essential for processing in vivo, while showing Lsm11 (not FLASH) activates the CPSF73 exonuclease mode.","evidence":"Drosophila null-rescue with point mutations, Y2H, Co-IP, scanning mutagenesis, and in vitro processing assays","pmids":["21525146","21245389"],"confidence":"High","gaps":["The additional processing factor recruited by FLASH/Lsm11 not identified at this point","Structural basis of the interaction unresolved"]},{"year":2012,"claim":"Revealed that the FLASH and Lsm11 N-termini form a platform recruiting the full polyadenylation machinery including CPSF73, unifying histone-specific and canonical 3'-end processing components.","evidence":"Reciprocal Co-IP, in vitro binding with point mutants, mass spectrometry, and histone pre-mRNA pulldown; independently replicated in Drosophila","pmids":["23071092","24145821"],"confidence":"High","gaps":["Stoichiometry and architecture of the platform not yet structural","How the docked endonuclease is positioned at the cleavage site unknown"]},{"year":2017,"claim":"Determined the stoichiometry and architecture of the FLASH-Lsm11 platform and assigned FLASH a second role in U7 recruitment, refining the order of complex assembly.","evidence":"X-ray crystallography, MALS, analytical ultracentrifugation, crosslinking, EMSA, and in vitro processing with SLBP/FLASH truncations","pmids":["29020104","28289156"],"confidence":"High","gaps":["Full Lsm11-containing U7 snRNP structure not yet solved","How the 2:1 platform engages the CPSF endonuclease structurally undefined"]},{"year":2019,"claim":"Added ALYREF as an Lsm11-interacting factor coupling U7 snRNP recruitment to downstream histone mRNA export.","evidence":"Co-IP, RNA-IP, and siRNA knockdown with processing and export assays","pmids":["30858280"],"confidence":"Medium","gaps":["Whether ALYREF acts on the same Lsm11 surface as FLASH unclear","Single-lab Co-IP without structural mapping"]},{"year":2020,"claim":"Connected LSM11 loss-of-function to human disease, showing histone misprocessing activates cGAS-STING interferon signaling in Aicardi-Goutières syndrome.","evidence":"Patient fibroblast studies, RT-PCR, cGAS immunofluorescence, in vitro cGAMP synthesis with reconstituted chromatin, and interferon assays","pmids":["33230297"],"confidence":"High","gaps":["How specific patient mutations impair the molecular steps not dissected","Tissue-specific consequences of disturbed linker histone stoichiometry unclear"]},{"year":2022,"claim":"Demonstrated in vivo that SMN-dependent Lsm10/Lsm11-mediated U7 snRNP assembly is required for neuromuscular junction integrity, extending Lsm11 function to SMA pathology.","evidence":"Mouse SMA model with AAV Lsm10/Lsm11 co-expression, RT-PCR, NMJ electrophysiology, immunofluorescence, and Agrin Western blot","pmids":["36130491"],"confidence":"High","gaps":["Mechanistic link from histone processing to Agrin loss not fully resolved","Why specific muscles are selectively vulnerable unknown"]},{"year":2023,"claim":"Resolved the structural and regulatory inputs to Lsm11: PRMT5 methylation of N-terminal arginines and a SUMO-interacting motif both govern U7 snRNP assembly.","evidence":"Cryo-EM of the Lsm10/Lsm11-methylosome, in vitro methylation, Co-IP; SUMO2 KO cells with SIM mutagenesis and rescue","pmids":["37562960","40639911"],"confidence":"Medium","gaps":["Functional consequence of Lsm11 arginine methylation on processing not fully defined","How SUMO interaction integrates with methylosome assembly unclear"]},{"year":2026,"claim":"Provided the structural mechanism by which Lsm11 activates cleavage, showing a conserved N-terminal helix contacts the CPSF73 endonuclease domain and is required for catalysis.","evidence":"Cryo-EM of reconstituted U7 snRNP on noncleavable pre-mRNA, helix mutagenesis, and in vitro cleavage assays","pmids":["41495886"],"confidence":"High","gaps":["How CPSF73 conformational activation is triggered in the productive cycle not fully resolved","Coordination of cleavage-site selection with the molecular ruler not structurally integrated"]},{"year":null,"claim":"How the multiple regulatory inputs to Lsm11 (PRMT5 methylation, SUMOylation, NPAT competition for FLASH) are integrated to control histone gene output across the cell cycle remains open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model coupling Lsm11 modifications to cleavage timing","Physiological role of Lsm11-NPAT competition for FLASH untested in vivo"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[6,12,15]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,7]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[11,21]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,8]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[5,8]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,6,12]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,6]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[17,18]}],"complexes":["U7 snRNP","FLASH-Lsm11 platform","histone cleavage complex (CPSF/CstF/symplekin)","PRMT5/MEP50/pICln methylosome"],"partners":["FLASH","LSM10","CPSF73","ZFP100","ALYREF","SLBP","PRMT5","SMN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P83369","full_name":"U7 snRNA-associated Sm-like protein LSm11","aliases":[],"length_aa":360,"mass_kda":39.5,"function":"Component of the U7 snRNP complex that is involved in the histone 3'-end pre-mRNA processing (PubMed:11574479, PubMed:16914750, PubMed:33230297). Increases U7 snRNA levels but not histone 3'-end pre-mRNA processing activity, when overexpressed (PubMed:11574479, PubMed:16914750). Required for cell cycle progression from G1 to S phases (By similarity). Binds specifically to the Sm-binding site of U7 snRNA (PubMed:11574479, PubMed:16914750)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P83369/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/LSM11","classification":"Common Essential","n_dependent_lines":1023,"n_total_lines":1208,"dependency_fraction":0.8468543046357616},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SMN1","stoichiometry":4.0},{"gene":"CLNS1A","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPF","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LSM11","total_profiled":1310},"omim":[{"mim_id":"619486","title":"AICARDI-GOUTIERES SYNDROME 8; AGS8","url":"https://www.omim.org/entry/619486"},{"mim_id":"617910","title":"LSM11, U7 SMALL NUCLEAR RNA-ASSOCIATED PROTEIN; LSM11","url":"https://www.omim.org/entry/617910"},{"mim_id":"617909","title":"LSM10, U7 SMALL NUCLEAR RNA-ASSOCIATED PROTEIN; LSM10","url":"https://www.omim.org/entry/617909"},{"mim_id":"617908","title":"ZINC FINGER PROTEIN 473; ZNF473","url":"https://www.omim.org/entry/617908"},{"mim_id":"606880","title":"CASPASE 8-ASSOCIATED PROTEIN 2; CASP8AP2","url":"https://www.omim.org/entry/606880"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in 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Its long N-terminal domain mediates an important step in histone mRNA 3'-end cleavage, while its C-terminal Sm motifs (interrupted by an unusually long spacer) are sufficient for assembly with U7 snRNA. Assembly of the U7-specific Sm core depends on the noncanonical Sm-binding site of U7 snRNA and is facilitated by a specialized SMN complex containing Lsm10 and Lsm11 but lacking SmD1/D2.\",\n      \"method\": \"In vitro assembly assays, immunoprecipitation, GST pulldown, in vitro processing assays, domain deletion/truncation analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro reconstitution of assembly, multiple domain truncations, functional processing assays, and reciprocal IPs; foundational study replicated by multiple subsequent labs\",\n      \"pmids\": [\"12975319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Drosophila Lsm11 (dLsm11) associates with dLsm10, SmB (but not SmD1/D2), and the Drosophila U7 snRNA, and indirectly with histone H3 pre-mRNA; dLsm10 and dLsm11 can assemble into U7 snRNPs in mammalian cells, demonstrating evolutionary conservation of the unique U7 snRNP composition.\",\n      \"method\": \"Immunoprecipitation in Drosophila S2 cells, cross-species complementation assay\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP in S2 cells and cross-species assembly assay, single lab\",\n      \"pmids\": [\"14624008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Lsm11 undergoes two distinct interactions with ZFP100: one between the Lsm11 N-terminus and the zinc finger repeats of ZFP100, and a second between the N-terminus of ZFP100 and the Sm domain of Lsm11. The second interaction is sufficient for specific recognition of U7 snRNP by ZFP100 in cell extracts. Clustered point mutations in three conserved regions of the Lsm11 N-terminus impair histone RNA processing independently of ZFP100 binding, indicating additional roles (e.g., contacting the pre-mRNA or other factors).\",\n      \"method\": \"GST pulldown (in vitro and in cell extracts), scanning mutagenesis, in vitro processing assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding assays with mutagenesis and functional processing readout, single lab\",\n      \"pmids\": [\"15824063\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Lsm10 and Lsm11 associate with the pICln subunit of the PRMT5 complex in vitro and in vivo without receiving symmetrical dimethylarginine (sDMA) modifications, implicating the PRMT5 complex in an early stage of U7 snRNP assembly independent of methylation. Binding of Lsm10 and Lsm11 to SMN is independent of methylation, and two separate binding sites exist in SMN: one recognizing Sm domains and one recognizing sDMA-modified RG-tails.\",\n      \"method\": \"Co-immunoprecipitation, GST pulldown, in vitro binding assays, methylation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP in cells plus in vitro pulldown, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"16087681\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"ZFP100 zinc fingers 5–10 are required for binding to a 20-amino-acid region of Lsm11, and the domain sufficient for Cajal body localization and Lsm11 binding is also sufficient to stimulate histone pre-mRNA processing in vivo, linking the ZFP100–Lsm11 interaction to processing activity.\",\n      \"method\": \"Co-immunoprecipitation, domain truncation, in vivo reporter assay, photobleaching (FRAP)\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, functional reporter, and domain mapping in a single lab\",\n      \"pmids\": [\"16714279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Lsm11 localizes to the histone locus body (HLB) in Drosophila embryos; using anti-Lsm11 antibodies, the HLB is shown to form at nuclear cycle 11 coincident with zygotic histone transcription. Lsm11 foci are present even in histone locus deletion embryos, indicating HLB assembly is not strictly dependent on the histone locus itself.\",\n      \"method\": \"Immunofluorescence, confocal microscopy, genetic ablation of histone locus in embryos\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by antibody staining with genetic controls, single lab\",\n      \"pmids\": [\"17442888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FLASH directly interacts with Lsm11 in vitro and in vivo (by yeast two-hybrid and immunoprecipitation), stimulates 3'-end processing of histone pre-mRNA in mammalian nuclear extracts, and is essential for U7-dependent processing in both vertebrates (human) and invertebrates (Drosophila), with FLASH depletion leading to polyadenylation of histone mRNAs.\",\n      \"method\": \"Yeast two-hybrid, GST pulldown (in vitro), co-immunoprecipitation (in vivo), in vitro processing assay (mammalian nuclear extracts), RNAi knockdown in Drosophila cells\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (Y2H, in vitro pulldown, reciprocal Co-IP, in vitro processing, in vivo RNAi) across two organisms; replicated by subsequent studies\",\n      \"pmids\": [\"19854135\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Three components of the U7-specific Sm ring—SmB, SmD3, and Lsm10—contact the region between the cleavage site and U7-binding site in histone pre-mRNA and likely function as a molecular ruler determining the cleavage site. Lsm11 and SmB were identified as stable components of the 3'-end processing complex assembled on histone pre-mRNA.\",\n      \"method\": \"Biotin-affinity pulldown of processing complex from nuclear extracts, UV cross-linking, mass spectrometry identification\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — affinity purification with UV cross-linking and mass spectrometry, single lab\",\n      \"pmids\": [\"19470752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Mutations in Drosophila Lsm11 disrupt histone pre-mRNA processing (causing polyadenylated histone mRNA). Lsm10 protein fails to accumulate in Lsm11 mutants, suggesting Lsm10–Lsm11 dimers are precursors for U7 snRNP assembly. Lsm11 is required for U7 snRNA localization to the histone locus body, even though U7 snRNA can still assemble into a trimethylguanosine-capped particle in the absence of Lsm11. Lsm10 and Lsm11 mutants, unlike U7 snRNA null mutants, are lethal, indicating an essential Lsm10/Lsm11 function beyond histone pre-mRNA processing.\",\n      \"method\": \"Drosophila genetics (null mutants), RT-PCR, immunofluorescence, anti-TMG immunoprecipitation\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function with molecular phenotyping, localization studies, and biochemical fractionation; multiple orthogonal methods\",\n      \"pmids\": [\"19620235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"CF Im68, a cleavage/polyadenylation factor, associates with highly purified U7 snRNP and this interaction depends on the N-terminus of Lsm11. Both depletion and overexpression of CF Im68 reduce histone RNA processing efficiency in vivo. The small CF Im subunit CF Im25 does not participate in histone RNA processing.\",\n      \"method\": \"Biochemical purification of U7 snRNP, immunoprecipitation, siRNA knockdown, in vitro processing assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — purification plus functional in vitro and in vivo assays, single lab\",\n      \"pmids\": [\"20634199\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Amino acids 105–154 of Drosophila FLASH bind to amino acids 1–78 of dLsm11 (N-terminal domain). A two-amino-acid mutation in dLsm11 that abolishes dFLASH binding, without affecting U7 snRNP localization to the HLB, fails to rescue lethality or processing defects caused by Lsm11 null mutation, demonstrating that the FLASH–Lsm11 protein–protein interaction is essential for histone pre-mRNA processing in vivo.\",\n      \"method\": \"Drosophila genetic rescue assay (null mutation complementation), yeast two-hybrid, co-immunoprecipitation, site-directed mutagenesis, immunofluorescence\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — genetic rescue with point mutations plus binding assays and localization; multiple orthogonal methods defining interaction domain and in vivo requirement\",\n      \"pmids\": [\"21525146\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Scanning mutagenesis identified critical residues in human Lsm11 that mediate its interaction with FLASH. Mutations in FLASH between residues 50–99 that do not affect Lsm11 binding convert FLASH into an inhibitory dominant negative, suggesting this FLASH region plus Lsm11 recruits an additional unknown processing factor. After endonucleolytic cleavage, the 5'→3' exonuclease activity of CPSF73 on the downstream cleavage product depends on Lsm11 but not on FLASH, indicating FLASH is dispensable for activating the exonuclease mode.\",\n      \"method\": \"Scanning mutagenesis, GST pulldown, in vitro processing assay with mammalian nuclear extracts, antibody inhibition\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro functional assay combined with systematic mutagenesis, single lab\",\n      \"pmids\": [\"21245389\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The N-terminal regions of FLASH and Lsm11 form a platform that recruits a specific set of polyadenylation factors—symplekin, CstF64, and all CPSF subunits including the CPSF73 endonuclease—to the U7 snRNP. Point mutations in FLASH that abolish processing also inhibit this interaction. The same polyadenylation factors associate with endogenous U7 snRNP and are recruited to histone pre-mRNA in a U7-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation (reciprocal), in vitro binding assays, point mutagenesis, mass spectrometry, histone pre-mRNA pull-down\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vitro binding with mutagenesis, mass spectrometry confirmation of endogenous complex; replicated in Drosophila by a subsequent independent study\",\n      \"pmids\": [\"23071092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The Drosophila U7 snRNP contains FLASH and at least six polyadenylation factors (symplekin, CPSF73, CPSF100, CPSF160, WDR33, CstF64) as stable stoichiometric components, and this composite particle is recruited to histone pre-mRNA for processing. A motif in Drosophila FLASH is essential for recruiting the polyadenylation complex to U7 snRNP via Lsm11.\",\n      \"method\": \"Biochemical purification from Drosophila nuclear extracts, mass spectrometry, RNAi knockdown, in vitro processing assay\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — biochemical purification with MS identification, functional RNAi, and in vitro processing; independent replication of mammalian findings in Drosophila\",\n      \"pmids\": [\"24145821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SLBP stabilizes U7 snRNP binding to histone pre-mRNA via two regions (helix B of its RNA-binding domain and C-terminal region), and this stabilization requires FLASH but not the downstream polyadenylation factors, assigning FLASH a second role: cooperating with SLBP to recruit U7 snRNP to histone pre-mRNA, distinct from its role in forming the polyadenylation factor docking platform with Lsm11.\",\n      \"method\": \"EMSA (gel shift), in vitro processing assay, domain truncation of SLBP/FLASH, UV cross-linking\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding and processing assays with domain truncations, single lab\",\n      \"pmids\": [\"28289156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structures of the FLASH N-terminal domain reveal it forms a coiled-coil dimer. Solution light scattering, analytical ultracentrifugation, and crosslinking show the FLASH NTD–Lsm11 NTD complex is a 2:1 heterotrimer (two FLASH NTD molecules per one Lsm11 NTD).\",\n      \"method\": \"X-ray crystallography, multi-angle light scattering, analytical ultracentrifugation, chemical crosslinking\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus multiple orthogonal biophysical methods to establish stoichiometry; single lab but rigorous\",\n      \"pmids\": [\"29020104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ALYREF physically interacts with Lsm11 (U7-snRNP-specific component) and promotes histone pre-mRNA 3'-end processing by facilitating U7-snRNP recruitment to histone pre-mRNA. ALYREF also enhances nuclear export of processed histone mRNAs as part of the TREX complex.\",\n      \"method\": \"Co-immunoprecipitation, RNA-immunoprecipitation, siRNA knockdown with processing and export assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and functional knockdown assays, single lab\",\n      \"pmids\": [\"30858280\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Biallelic mutations in LSM11 (encoding a component of the U7 snRNP histone pre-mRNA processing complex) cause misprocessing of canonical histone transcripts, disturb linker histone stoichiometry, alter nuclear cGAS distribution, and enhance cGAS-STING-mediated type I interferon signaling, establishing LSM11 as an Aicardi-Goutières syndrome gene. Chromatin lacking linker histone stimulates cGAMP production more efficiently in vitro, linking histone processing defects to innate immune activation.\",\n      \"method\": \"Patient-derived fibroblast studies, RT-PCR (histone mRNA processing), cGAS localization (immunofluorescence), cGAS in vitro cGAMP synthesis assay with reconstituted chromatin, interferon signaling assays\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods in patient cells plus in vitro mechanistic reconstitution; published in a high-scrutiny journal\",\n      \"pmids\": [\"33230297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SMN-mediated assembly of U7 snRNP (requiring Lsm10 and Lsm11) is necessary for neuromuscular junction (NMJ) integrity; co-expression of Lsm10 and Lsm11 selectively enhances U7 snRNP assembly, corrects histone mRNA processing defects, and rescues NMJ denervation, synaptic transmission defects, and skeletal muscle atrophy in SMA mice. U7 snRNP dysfunction also drives selective loss of the synaptic organizer Agrin at NMJs in vulnerable muscles.\",\n      \"method\": \"Mouse SMA model (in vivo), AAV-mediated co-expression of Lsm10/Lsm11, RT-PCR (histone mRNA processing), electrophysiology (NMJ transmission), immunofluorescence (NMJ morphology), Western blot (Agrin levels)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo rescue with Lsm10/Lsm11, multiple orthogonal functional readouts, mouse model with rigorous controls\",\n      \"pmids\": [\"36130491\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A heterodimer of Lsm10 and Lsm11 tightly interacts with the PRMT5/MEP50/pICln methylosome. Cryo-EM structural studies and biochemical assays show the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the N-terminal region of Lsm11. PRMT5 also methylates an N-terminal arginine in SmE specifically in the U7 context (SmE is not methylated during spliceosomal Sm ring biogenesis).\",\n      \"method\": \"Cryo-EM structure determination, in vitro methylation assay, co-immunoprecipitation, biochemical binding assays\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure plus in vitro enzymatic assay and biochemical binding; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"37562960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A SUMO-interacting motif (SIM) in the N-terminus of Lsm11 is required for efficient formation of U7 snRNP; in SUMO2 knockout cells, U7 snRNP levels are reduced and histone pre-mRNA 3'-end cleavage is defective with increased histone mRNA polyadenylation. Overexpression of Lsm11 and U7 snRNA rescues U7 snRNP levels and processing defects in SUMO2 KO cells.\",\n      \"method\": \"SUMO2 knockout cell line, rescue by Lsm11/U7 snRNA overexpression, RT-PCR (histone mRNA processing), immunofluorescence (HLB dynamics), SIM deletion mutagenesis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO cell line with mutagenesis and rescue, multiple functional readouts; single lab\",\n      \"pmids\": [\"40639911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"A conserved N-terminal helix of Lsm11 contacts the metallo-β-lactamase domain of the CPSF73 endonuclease within U7 snRNP; mutating or deleting this helix substantially reduces cleavage activity toward histone pre-mRNA. Cryo-EM of reconstituted wild-type U7 snRNP on a noncleavable pre-mRNA shows CPSF73 can adopt an open, active conformation independent of RNA binding at its active site. The CstF77 C-terminus contacts the CPSF100 subunit at a newly identified binding site that modestly contributes to cleavage activity.\",\n      \"method\": \"Cryo-EM structure determination, site-directed mutagenesis (helix deletion/point mutants), in vitro cleavage assay, reconstitution of U7 snRNP with pre-mRNA\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure plus mutagenesis and in vitro activity reconstitution; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"41495886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Hydrogen/deuterium exchange mass spectrometry shows the FLASH-interacting domain in Lsm11 is highly dynamic, while a downstream region required for recruiting the histone cleavage complex (HCC) folds into a stable structure. In vitro binding assays reveal Lsm11 also contacts the C-terminal SANT/Myb-like domain of FLASH (the same region that binds NPAT), and this binding partially relaxes (destabilizes) that domain, suggesting competition between Lsm11 and NPAT for FLASH that may regulate histone gene expression.\",\n      \"method\": \"Hydrogen/deuterium exchange mass spectrometry, in vitro GST pulldown binding assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — HDX-MS plus in vitro binding assays; single lab, two orthogonal methods\",\n      \"pmids\": [\"26860583\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LSM11 is a U7 snRNP-specific Sm-like protein that replaces SmD2 in the heptameric Sm ring; its N-terminal extension (stabilized by a conserved helix that contacts CPSF73, and methylated by PRMT5 via a PRMT5-Lsm10/Lsm11 interaction) docks FLASH in a 2:1 FLASH:Lsm11 heterotrimer, which together recruit the CPSF73 endonuclease and associated polyadenylation factors (symplekin, CstF64, CPSF subunits) to catalyze endonucleolytic 3'-end cleavage of replication-dependent histone pre-mRNAs; loss of functional Lsm11 causes histone mRNA misprocessing, disrupts linker histone stoichiometry, activates cGAS-STING-mediated type I interferon signaling (causing Aicardi-Goutières syndrome), and impairs neuromuscular junction integrity in SMA models.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LSM11 is a U7 snRNP-specific Sm-like protein that constitutes the catalytic engine for endonucleolytic 3'-end cleavage of replication-dependent histone pre-mRNAs [#0, #6]. It replaces SmD2 in the heptameric Sm ring, assembling with Lsm10 onto the noncanonical Sm-binding site of U7 snRNA via a specialized SMN complex; its C-terminal Sm motifs (split by a long spacer) drive ring assembly while its extended N-terminal domain carries the processing function [#0]. This N-terminal domain docks FLASH, forming a 2:1 FLASH:Lsm11 heterotrimer whose paired N-terminal regions build a platform that recruits the cleavage/polyadenylation machinery\\u2014symplekin, CstF64, and the CPSF subunits including the CPSF73 endonuclease\\u2014to the U7 snRNP [#12, #15]. A conserved N-terminal helix of Lsm11 directly contacts the metallo-\\u03b2-lactamase domain of CPSF73 and is required for efficient cleavage, and CPSF73 exonuclease activity on the downstream product depends on Lsm11 [#11, #21]. Assembly and activity of this machinery are governed by additional layers: PRMT5 methylates two arginines in the Lsm11 N-terminus and tethers the Lsm10/Lsm11 heterodimer to the methylosome [#19], a SUMO-interacting motif promotes efficient U7 snRNP formation [#20], and the particle is recruited to histone pre-mRNA cooperatively with SLBP, FLASH, and ALYREF [#14, #16]. Biallelic LSM11 mutations cause Aicardi-Gouti\\u00e8res syndrome by misprocessing histone transcripts, disturbing linker histone stoichiometry, and activating cGAS-STING type I interferon signaling [#17].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established that LSM11 is a U7 snRNP-specific Sm-like protein with a functional division of labor between its domains, answering what distinguishes the histone-processing snRNP from spliceosomal snRNPs.\",\n      \"evidence\": \"In vitro assembly, IP, GST pulldown, and processing assays with domain truncations; cross-species Co-IP in Drosophila S2 cells\",\n      \"pmids\": [\"12975319\", \"14624008\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of how the N-terminal domain drives cleavage not defined at this stage\", \"Direct cleavage factors recruited by Lsm11 not yet identified\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Mapped Lsm11 N-terminal interactions with ZFP100 and the PRMT5/pICln complex, beginning to define how the U7 snRNP recognizes processing partners and is routed through assembly.\",\n      \"evidence\": \"GST pulldown, scanning mutagenesis, in vitro processing, and Co-IP/methylation assays\",\n      \"pmids\": [\"15824063\", \"16087681\", \"16714279\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ZFP100 interaction later superseded as the key processing tether by FLASH\", \"Functional consequence of PRMT5 association on Lsm11 not resolved here\", \"Additional N-terminal contacts inferred but partners unidentified\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Localized Lsm11 to the histone locus body, linking the protein to the nuclear compartment where histone gene expression is organized.\",\n      \"evidence\": \"Immunofluorescence and confocal microscopy in Drosophila embryos with histone locus genetic ablation\",\n      \"pmids\": [\"17442888\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"What nucleates HLB assembly independent of the histone locus unknown\", \"Role of Lsm11 in HLB formation vs. recruitment not separated\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified FLASH as the essential Lsm11-binding factor for processing and showed Lsm11 is required in vivo for U7 snRNP function and viability beyond histone processing.\",\n      \"evidence\": \"Y2H, GST pulldown, reciprocal Co-IP, in vitro processing, RNAi, and Drosophila null mutant genetics with molecular phenotyping\",\n      \"pmids\": [\"19854135\", \"19620235\", \"19470752\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How FLASH-Lsm11 enables cleavage not yet mechanistic\", \"Identity of the essential non-processing Lsm10/Lsm11 function undefined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defined the FLASH-Lsm11 interaction at residue resolution and proved by genetic rescue that this protein-protein contact is essential for processing in vivo, while showing Lsm11 (not FLASH) activates the CPSF73 exonuclease mode.\",\n      \"evidence\": \"Drosophila null-rescue with point mutations, Y2H, Co-IP, scanning mutagenesis, and in vitro processing assays\",\n      \"pmids\": [\"21525146\", \"21245389\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The additional processing factor recruited by FLASH/Lsm11 not identified at this point\", \"Structural basis of the interaction unresolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealed that the FLASH and Lsm11 N-termini form a platform recruiting the full polyadenylation machinery including CPSF73, unifying histone-specific and canonical 3'-end processing components.\",\n      \"evidence\": \"Reciprocal Co-IP, in vitro binding with point mutants, mass spectrometry, and histone pre-mRNA pulldown; independently replicated in Drosophila\",\n      \"pmids\": [\"23071092\", \"24145821\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and architecture of the platform not yet structural\", \"How the docked endonuclease is positioned at the cleavage site unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Determined the stoichiometry and architecture of the FLASH-Lsm11 platform and assigned FLASH a second role in U7 recruitment, refining the order of complex assembly.\",\n      \"evidence\": \"X-ray crystallography, MALS, analytical ultracentrifugation, crosslinking, EMSA, and in vitro processing with SLBP/FLASH truncations\",\n      \"pmids\": [\"29020104\", \"28289156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full Lsm11-containing U7 snRNP structure not yet solved\", \"How the 2:1 platform engages the CPSF endonuclease structurally undefined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Added ALYREF as an Lsm11-interacting factor coupling U7 snRNP recruitment to downstream histone mRNA export.\",\n      \"evidence\": \"Co-IP, RNA-IP, and siRNA knockdown with processing and export assays\",\n      \"pmids\": [\"30858280\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ALYREF acts on the same Lsm11 surface as FLASH unclear\", \"Single-lab Co-IP without structural mapping\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Connected LSM11 loss-of-function to human disease, showing histone misprocessing activates cGAS-STING interferon signaling in Aicardi-Gouti\\u00e8res syndrome.\",\n      \"evidence\": \"Patient fibroblast studies, RT-PCR, cGAS immunofluorescence, in vitro cGAMP synthesis with reconstituted chromatin, and interferon assays\",\n      \"pmids\": [\"33230297\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How specific patient mutations impair the molecular steps not dissected\", \"Tissue-specific consequences of disturbed linker histone stoichiometry unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated in vivo that SMN-dependent Lsm10/Lsm11-mediated U7 snRNP assembly is required for neuromuscular junction integrity, extending Lsm11 function to SMA pathology.\",\n      \"evidence\": \"Mouse SMA model with AAV Lsm10/Lsm11 co-expression, RT-PCR, NMJ electrophysiology, immunofluorescence, and Agrin Western blot\",\n      \"pmids\": [\"36130491\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link from histone processing to Agrin loss not fully resolved\", \"Why specific muscles are selectively vulnerable unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolved the structural and regulatory inputs to Lsm11: PRMT5 methylation of N-terminal arginines and a SUMO-interacting motif both govern U7 snRNP assembly.\",\n      \"evidence\": \"Cryo-EM of the Lsm10/Lsm11-methylosome, in vitro methylation, Co-IP; SUMO2 KO cells with SIM mutagenesis and rescue\",\n      \"pmids\": [\"37562960\", \"40639911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of Lsm11 arginine methylation on processing not fully defined\", \"How SUMO interaction integrates with methylosome assembly unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Provided the structural mechanism by which Lsm11 activates cleavage, showing a conserved N-terminal helix contacts the CPSF73 endonuclease domain and is required for catalysis.\",\n      \"evidence\": \"Cryo-EM of reconstituted U7 snRNP on noncleavable pre-mRNA, helix mutagenesis, and in vitro cleavage assays\",\n      \"pmids\": [\"41495886\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How CPSF73 conformational activation is triggered in the productive cycle not fully resolved\", \"Coordination of cleavage-site selection with the molecular ruler not structurally integrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the multiple regulatory inputs to Lsm11 (PRMT5 methylation, SUMOylation, NPAT competition for FLASH) are integrated to control histone gene output across the cell cycle remains open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model coupling Lsm11 modifications to cleavage timing\", \"Physiological role of Lsm11-NPAT competition for FLASH untested in vivo\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [6, 12, 15]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [11, 21]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 8]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [5, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 6, 12]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [17, 18]}\n    ],\n    \"complexes\": [\"U7 snRNP\", \"FLASH-Lsm11 platform\", \"histone cleavage complex (CPSF/CstF/symplekin)\", \"PRMT5/MEP50/pICln methylosome\"],\n    \"partners\": [\"FLASH\", \"LSM10\", \"CPSF73\", \"ZFP100\", \"ALYREF\", \"SLBP\", \"PRMT5\", \"SMN\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":6,"faith_total":6,"faith_pct":100.0}}