{"gene":"H1-5","run_date":"2026-06-10T01:55:21","timeline":{"discoveries":[{"year":2004,"finding":"MSX1 physically interacts with histone H1b (H1-5 mouse ortholog) and together they bind to a key regulatory element of MyoD, inducing repressed chromatin and cooperating to inhibit skeletal muscle differentiation in cell culture and Xenopus animal caps.","method":"Physical interaction identified by co-immunoprecipitation/pulldown; chromatin binding demonstrated by ChIP; functional cooperation shown by cell culture and Xenopus animal cap assays","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, ChIP, and functional loss-of-function in two independent systems (cell culture and Xenopus)","pmids":["15192231"],"is_preprint":false},{"year":2012,"finding":"H1.5 binds genic and intergenic regions in differentiated human cells (but not embryonic stem cells), preferentially at membrane-related gene families; H1.5 binding is required for SIRT1 binding, H3K9me2 enrichment, and chromatin compaction. Depletion of H1.5 causes loss of SIRT1 and H3K9me2, increased chromatin accessibility, deregulation of gene expression, and decreased cell growth.","method":"ChIP-seq for H1.5 genomic distribution; siRNA-mediated knockdown with ChIP for SIRT1 and H3K9me2, chromatin accessibility assays, gene expression profiling, and cell growth assays","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (ChIP-seq, KD, histone mark analysis, chromatin accessibility) in a single rigorous study","pmids":["22956909"],"is_preprint":false},{"year":2009,"finding":"H1.5 undergoes site-specific phosphorylation at distinct residues during the cell cycle: Ser(17) and Ser(172) appear in interphase at DNA replication and transcription sites, while Thr(10) phosphorylation begins in prophase and peaks in metaphase on chromatin-bound H1.5, disappearing before chromatin decondensation. Different kinases are implicated at different sites (staurosporine sensitivity).","method":"Affinity-purified phosphosite-specific polyclonal antibodies; immunofluorescence in synchronized HeLa cells; kinase inhibitor (staurosporine) treatment; colocalization with replication/transcription markers","journal":"Chromosoma","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — specific antibody-based imaging in synchronized cells with inhibitor validation, single lab","pmids":["19609548"],"is_preprint":false},{"year":2008,"finding":"GSK-3 phosphorylates H1.5 at threonine 10 during M phase. This phosphorylation appears in prometaphase and disappears in telophase; the hyperphosphorylated form is mainly chromatin-bound in metaphase. GSK-3 inhibitors reduce Thr10 phosphorylation both in vitro and in vivo; CDK1/cyclin B and CDK5/p35 do not phosphorylate this site.","method":"In vitro kinase assays with GSK-3, CDK1/cyclin B, and CDK5/p35; immunofluorescence with phosphospecific antiserum in HeLa cells; GSK-3 inhibitor treatment in cells","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay identifying the writer, confirmed in vivo with inhibitors, negative controls for other kinases included","pmids":["19136008"],"is_preprint":false},{"year":1997,"finding":"H1b (H1-5 mouse ortholog) selectively binds the Omega regulatory element within the coding region of the replication-dependent H3.2 histone gene with ~100-fold higher affinity than the comparable sequence of the replication-independent H3.3 gene, suggesting a specific role in regulating replication-dependent histone gene expression.","method":"In vitro binding assays (gel mobility shift/footprinting) comparing H1b affinity for H3.2 vs H3.3 Omega sequences","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding assay with sequence specificity demonstrated, single lab","pmids":["9182532"],"is_preprint":false},{"year":1997,"finding":"Phosphorylation of H1b (H1-5 mouse ortholog) is dependent on ongoing transcription and replication: inhibition of transcription (actinomycin D, DRB) or replication (aphidicolin) markedly decreases pH1b levels, and phosphorylation is restored after removal of DRB. This suggests pH1b is associated with transcribing chromatin and that phosphorylation may facilitate chromatin decondensation for transcription and replication.","method":"Pharmacological inhibition of transcription and replication in normal and ras-transformed mouse fibroblasts; quantification of pH1b by Western blot/immunological methods","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological perturbation with functional readout, single lab, two inhibitors for transcription tested","pmids":["9079620"],"is_preprint":false},{"year":2019,"finding":"H1.5 binds DNA over splice sites of short exons in human lung fibroblasts, and this binding correlates with inclusion of alternatively spliced exons. Depletion of H1.5 decreases exon inclusion and reduces RNA polymerase II levels over these exons, indicating H1.5 regulates alternative splicing through RNAP II stalling near 3' splice sites.","method":"ChIP-seq for H1.5 binding at splice sites; siRNA knockdown of H1.5; RT-PCR for exon inclusion; ChIP for RNAP II occupancy","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP-seq, functional knockdown, and RNAP II ChIP as orthogonal mechanistic methods in a single study","pmids":["31076740"],"is_preprint":false},{"year":2016,"finding":"Differences in chromatin-binding affinity between H1.1 (lower) and H1.5 (higher) were mapped by in vitro mutagenesis to a single amino acid polymorphism near the junction of the globular and C-terminal domains. Overexpression of H1.5 in density-arrested fibroblasts did not affect cell cycle progression after release.","method":"FRAP (fluorescence recovery after photobleaching) to measure exchange rates; in vitro mutagenesis; cell cycle analysis after H1 overexpression","journal":"Biology open","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro mutagenesis with FRAP readout, single lab study","pmids":["26912777"],"is_preprint":false},{"year":2013,"finding":"H1.5 (along with H1.2–H1.4) is depleted from CpG-dense regions and active regulatory regions in human lung fibroblasts, while it marks specific repressive domains, implicating H1.5 in three-dimensional genome organization.","method":"DamID (DNA adenine methyltransferase identification) genome-wide mapping of all five somatic H1 subtypes","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide DamID mapping, single lab, cross-subtype comparison","pmids":["23746450"],"is_preprint":false},{"year":2004,"finding":"Monoubiquitinated H1B is secreted from HRF+ CD4+ T cells resistant to HIV-1. Specific siRNA silencing of H1B in HRF+ cells reduced antiviral activity of supernatants by 96% and reversed the HIV-1 resistance phenotype, establishing H1B as a required cofactor for HRF-mediated antiviral protection.","method":"RNAi knockdown of H1B; Western blot with anti-H1 and anti-ubiquitin antibodies; antiviral activity assays on cell culture supernatants","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNAi knockdown with functional antiviral assay readout, single lab","pmids":["15610014"],"is_preprint":false},{"year":2019,"finding":"Ras-AKT signaling represses phosphorylation of H1.5 at Thr10 through MDM2-dependent degradation of GSK3, thereby promoting glioma cell growth and migration. Overexpression of H1.5-T10ph inhibits Ras-driven growth and migration, and H1.5-T10ph regulates transcription of Ras downstream genes (CYR61, IGFBP3, WNT16B, NT5E, GDF15, CARD16).","method":"Plasmid transfection of Ras/AKT constructs; Western blot for phospho-H1.5-T10 and phospho-AKT; MTT, soft-agar colony formation, transwell migration assays; qRT-PCR and ChIP assay for downstream gene regulation","journal":"Artificial cells, nanomedicine, and biotechnology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays and ChIP, single lab, pathway placement by epistasis","pmids":["31307224"],"is_preprint":false},{"year":2024,"finding":"FOXM1 binds the H1B promoter region and regulates H1B expression in human epidermal stem cells. H1B in turn binds the promoter regions of differentiation-related genes and negatively regulates their expression, placing H1B downstream of FOXM1 in a pathway controlling self-renewal versus differentiation.","method":"Single-cell transcriptomics; ChIP assay (FOXM1 binding to H1B promoter; H1B binding to differentiation gene promoters); enforced FOXM1 expression experiments; analysis of H1B expression across clonal types","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and functional overexpression experiments, single lab","pmids":["39019868"],"is_preprint":false},{"year":2021,"finding":"HIST1H1B (H1-5) upregulates CSF2 (colony-stimulating factor 2) expression by binding the CSF2 promoter in basal-like breast cancer cells, thereby promoting tumor growth and migration. Knockdown of HIST1H1B suppresses tumorigenicity.","method":"ChIP assay for H1B binding at CSF2 promoter; transwell, colony formation, and mammosphere assays; tumorigenesis assays; qRT-PCR","journal":"Frontiers in oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP linking H1B to CSF2 promoter, knockdown with functional tumorigenesis readout, single lab","pmids":["34746019"],"is_preprint":false},{"year":2024,"finding":"H1.5 is universally enriched at the nuclear periphery and co-localizes with compacted DNA in all human cell lines examined. Knockdown of H1.5 (alone or combined) does not trigger global chromatin decompaction, whereas H1.2 knockdown does; the depletion of H1.5 causes variant-specific chromatin structure alterations.","method":"Super-resolution microscopy and immunofluorescence imaging of H1 variants; siRNA knockdown; chromatin structure assays","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct imaging with super-resolution and functional knockdown, single lab, multiple cell lines","pmids":["38530350"],"is_preprint":false},{"year":2025,"finding":"H1.5 directly interacts with CENP-A mononucleosomes in vitro and localizes to centromeres in human cells. ChIP confirms interaction between H1.5 and centromeric chromatin. Knockdown of H1.5 results in loss of centromeric α-satellite transcription, reduced loading of new CENP-A, altered kinetochore protein gene expression, and accumulation of mitotic defects.","method":"In vitro binding assays with CENP-A mononucleosomes; immunofluorescence localization; ChIP; siRNA knockdown with analysis of CENP-A loading, α-satellite transcription, and mitotic defects","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution, ChIP in vivo, and functional knockdown with multiple orthogonal readouts; peer-reviewed publication","pmids":["41521667"],"is_preprint":false}],"current_model":"H1-5 (H1.5/H1b) is a linker histone that compacts chromatin at the nuclear periphery and specific gene loci by interacting with CENP-A nucleosomes at centromeres (required for CENP-A loading and mitotic integrity), recruiting SIRT1 and H3K9me2 to repress defined gene families, binding splice-site DNA to slow RNA polymerase II and regulate alternative splicing, and cooperating with transcription factors such as MSX1 (to repress MyoD) and acting downstream of FOXM1 (to silence differentiation genes); its activity is modulated by cell-cycle-regulated, site-specific phosphorylation—with GSK-3 phosphorylating Thr10 in M phase and Ras-AKT-MDM2 suppressing this modification—as well as by monoubiquitination that enables its secretion as a cofactor in antiviral responses."},"narrative":{"mechanistic_narrative":"H1-5 (H1.5/H1b) is a somatic linker histone that organizes higher-order chromatin structure and acts as a locus-specific transcriptional repressor in differentiated cells [PMID:22956909, PMID:38530350]. It is enriched at the nuclear periphery in association with compacted DNA, and in differentiated (but not embryonic stem) cells it binds defined genic and intergenic domains—preferentially membrane-related gene families—where its presence is required for recruitment of SIRT1, enrichment of repressive H3K9me2, and chromatin compaction; depletion increases chromatin accessibility, deregulates gene expression, and slows cell growth [PMID:22956909, PMID:38530350]. H1-5 directs gene silencing through cooperation with sequence-specific factors, repressing MyoD together with the homeoprotein MSX1 to block muscle differentiation [PMID:15192231] and acting downstream of FOXM1 to bind and repress differentiation-gene promoters in epidermal stem cells, thereby balancing self-renewal against differentiation [PMID:39019868]. Beyond steady-state chromatin, it binds DNA over short-exon splice sites and slows RNA polymerase II near 3' splice sites to promote exon inclusion, coupling chromatin to alternative splicing [PMID:31076740], and it directly interacts with CENP-A nucleosomes at centromeres where it is required for α-satellite transcription, new CENP-A loading, and mitotic fidelity [PMID:41521667]. H1-5 activity is regulated by cell-cycle, site-specific phosphorylation: GSK-3 phosphorylates Thr10 on chromatin-bound H1.5 from prometaphase to telophase, and Ras-AKT signaling suppresses this mark via MDM2-dependent GSK3 degradation to promote glioma growth [PMID:19136008, PMID:31307224]. In disease contexts it has been linked to oncogenic transcription, upregulating CSF2 in basal-like breast cancer to drive tumorigenicity [PMID:34746019].","teleology":[{"year":1997,"claim":"Established that the linker histone H1b has intrinsic DNA-sequence selectivity rather than acting only as a generic chromatin compactor, and that its phosphorylation tracks active genome processes.","evidence":"In vitro binding assays comparing affinity for H3.2 vs H3.3 Omega elements, and pharmacological inhibition of transcription/replication with pH1b quantification in mouse fibroblasts","pmids":["9182532","9079620"],"confidence":"Medium","gaps":["In vitro sequence preference not validated genome-wide","Kinase responsible for transcription/replication-linked phosphorylation not identified","Functional consequence of H3.2 gene binding in vivo untested"]},{"year":2004,"claim":"Showed that H1-5 represses specific genes by partnering with a sequence-specific transcription factor, defining a targeted rather than purely structural role.","evidence":"Co-IP, ChIP, and functional differentiation assays of MSX1–H1b at the MyoD locus in cell culture and Xenopus animal caps","pmids":["15192231"],"confidence":"High","gaps":["Whether MSX1 recruits H1b or vice versa unresolved","Generality beyond MyoD unknown at the time","No structural basis for the interaction"]},{"year":2004,"claim":"Revealed an unexpected extracellular role: monoubiquitinated H1B is secreted and required for HRF-mediated antiviral protection, extending H1-5 function beyond chromatin.","evidence":"siRNA silencing of H1B in HRF+ CD4+ T cells with antiviral activity assays on supernatants and anti-ubiquitin Western blots","pmids":["15610014"],"confidence":"Medium","gaps":["Mechanism of secretion and ubiquitination not defined","Single-system observation not independently confirmed","Molecular target of secreted H1B in antiviral activity unknown"]},{"year":2009,"claim":"Defined H1.5 as a phosphorylation-regulated histone with distinct interphase and mitotic phosphosites, linking specific modifications to replication, transcription, and mitotic chromatin states.","evidence":"Phosphosite-specific antibodies and immunofluorescence in synchronized HeLa cells with staurosporine and replication/transcription marker colocalization","pmids":["19609548"],"confidence":"Medium","gaps":["Kinases for Ser17/Ser172 not identified","Functional consequence of each phosphosite not tested","Antibody-based localization without orthogonal confirmation"]},{"year":2008,"claim":"Identified GSK-3 as the writer of the mitotic Thr10 mark, placing H1.5 phosphorylation under a defined kinase and excluding alternative mitotic kinases.","evidence":"In vitro kinase assays with GSK-3, CDK1/cyclinB, CDK5/p35 plus phosphospecific immunofluorescence and GSK-3 inhibition in HeLa cells","pmids":["19136008"],"confidence":"High","gaps":["Downstream effect of Thr10ph on chromatin function not established here","Upstream control of GSK-3 toward H1.5 unknown","Whether Thr10ph alters DNA/nucleosome binding untested"]},{"year":2012,"claim":"Provided the genome-wide mechanistic picture: H1.5 binding in differentiated cells nucleates a repressive SIRT1/H3K9me2 compaction module at specific gene families.","evidence":"ChIP-seq of H1.5 with siRNA knockdown and ChIP for SIRT1/H3K9me2, chromatin accessibility, expression and growth assays in human cells","pmids":["22956909"],"confidence":"High","gaps":["Order of recruitment of H1.5, SIRT1, H3K9me2 not resolved","Why ESCs lack H1.5 binding unexplained","Direct vs indirect dependence of SIRT1 on H1.5 not separated"]},{"year":2013,"claim":"Mapped H1.5 within the broader linker-histone repertoire, showing depletion from active/CpG-dense regions and enrichment in repressive domains, implicating it in 3D genome organization.","evidence":"DamID genome-wide mapping of all five somatic H1 subtypes in human lung fibroblasts","pmids":["23746450"],"confidence":"Medium","gaps":["Functional consequence of repressive-domain marking not tested","Subtype-specific contribution not isolated by perturbation","Relationship to nuclear-periphery localization not directly linked"]},{"year":2016,"claim":"Traced H1.5's higher chromatin-binding affinity to a single residue near the globular/C-terminal junction, providing a molecular determinant of variant-specific behavior.","evidence":"FRAP exchange-rate measurements with in vitro mutagenesis and cell-cycle analysis after overexpression","pmids":["26912777"],"confidence":"Medium","gaps":["Affinity difference not connected to a downstream function","Overexpression showed no cell-cycle effect, leaving phenotype unclear","Single-residue effect not tested in chromatin context genome-wide"]},{"year":2019,"claim":"Extended H1.5 function to co-transcriptional RNA processing, showing it controls alternative splicing by stalling RNAP II at splice sites of short exons.","evidence":"ChIP-seq of H1.5 at splice sites, siRNA knockdown, RT-PCR for exon inclusion, and RNAP II ChIP in human lung fibroblasts","pmids":["31076740"],"confidence":"High","gaps":["Mechanism by which H1.5 stalls RNAP II not defined","Whether splicing role depends on its repressive partners unknown","Spliceosome interplay not characterized"]},{"year":2019,"claim":"Placed H1.5-T10 phosphorylation in an oncogenic signaling axis, showing Ras-AKT-MDM2 suppresses the mark to relieve repression of Ras target genes and promote glioma growth.","evidence":"Ras/AKT transfection with phospho-H1.5-T10 Western blot, growth/migration assays, and ChIP/qRT-PCR for downstream genes","pmids":["31307224"],"confidence":"Medium","gaps":["Direct binding of H1.5-T10ph to target promoters vs indirect effect not separated","GSK3 degradation mechanism by MDM2 not structurally defined","Findings restricted to glioma model"]},{"year":2021,"claim":"Demonstrated a gene-activating, pro-tumorigenic role in breast cancer, contrasting with H1.5's repressive functions elsewhere.","evidence":"ChIP at CSF2 promoter, knockdown with colony/mammosphere/tumorigenesis assays in basal-like breast cancer cells","pmids":["34746019"],"confidence":"Medium","gaps":["How a linker histone activates CSF2 not mechanistically explained","Cofactors at the CSF2 promoter not identified","Context-dependence vs repressive role unresolved"]},{"year":2024,"claim":"Positioned H1B in a FOXM1-driven self-renewal/differentiation circuit, showing it is a transcriptional effector repressing differentiation genes in epidermal stem cells.","evidence":"scRNA-seq, ChIP for FOXM1→H1B promoter and H1B→differentiation-gene promoters, and enforced FOXM1 expression","pmids":["39019868"],"confidence":"Medium","gaps":["Whether H1B repression uses the SIRT1/H3K9me2 module here untested","Direct FOXM1–H1B regulatory step vs indirect not fully isolated","In vivo requirement not established"]},{"year":2024,"claim":"Established universal nuclear-periphery enrichment and variant-specific, non-redundant chromatin roles distinguishing H1.5 from H1.2.","evidence":"Super-resolution imaging and siRNA knockdown of H1 variants across multiple human cell lines","pmids":["38530350"],"confidence":"Medium","gaps":["Molecular basis of variant-specific effects not defined","Why H1.5 KD does not globally decompact unexplained","Periphery-tethering mechanism unknown"]},{"year":2025,"claim":"Identified a direct centromeric function: H1.5 binds CENP-A nucleosomes and is required for α-satellite transcription, CENP-A loading, and mitotic integrity.","evidence":"In vitro binding to CENP-A mononucleosomes, immunofluorescence, ChIP, and siRNA knockdown with CENP-A loading and mitotic-defect readouts","pmids":["41521667"],"confidence":"High","gaps":["Structural basis of H1.5–CENP-A interaction not solved","How H1.5 promotes α-satellite transcription mechanistically unclear","Relationship to Thr10 mitotic phosphorylation not linked"]},{"year":null,"claim":"How a single linker histone reconciles opposing context-dependent outputs—peripheral compaction and repression, RNAP II stalling for splicing, centromeric CENP-A support, and gene activation in cancer—remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model linking phosphorylation/ubiquitination state to functional switching","Direct interactome at distinct loci not comprehensively defined","Structural mechanism of CENP-A and splice-site DNA recognition unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[4,6,14]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,1,11,12]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[1,13]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[14]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2,13]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[3,13]},{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[13]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[14]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[1,8,13]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,11,12]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[6]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[2,3,14]}],"complexes":[],"partners":["MSX1","SIRT1","CENP-A","FOXM1","GSK3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P16401","full_name":"Histone H1.5","aliases":["Histone H1a","Histone H1b","Histone H1s-3"],"length_aa":226,"mass_kda":22.6,"function":"Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber (By similarity). Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers and promote formation of the H3K27me3 mark by the PRC2/EED-EZH2 complex (PubMed:40516528). Also acts as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity)","subcellular_location":"Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/P16401/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/H1-5","classification":"Not Classified","n_dependent_lines":7,"n_total_lines":1208,"dependency_fraction":0.005794701986754967},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"AP2S1","stoichiometry":4.0},{"gene":"CNBP","stoichiometry":0.2},{"gene":"PABPC4","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/H1-5","total_profiled":1310},"omim":[{"mim_id":"602831","title":"H4 CLUSTERED HISTONE 13; H4C13","url":"https://www.omim.org/entry/602831"},{"mim_id":"602814","title":"HISTONE GENE CLUSTER 1, H3 HISTONE FAMILY, MEMBER I; HIST1H3I","url":"https://www.omim.org/entry/602814"},{"mim_id":"602793","title":"HISTONE GENE CLUSTER 1, H2A HISTONE FAMILY, MEMBER L; HIST1H2AL","url":"https://www.omim.org/entry/602793"},{"mim_id":"142712","title":"HISTONE GENE CLUSTER 1, H1 HISTONE FAMILY, MEMBER T; HIST1H1T","url":"https://www.omim.org/entry/142712"},{"mim_id":"142711","title":"HISTONE GENE CLUSTER 1, H1 HISTONE FAMILY, MEMBER B; HIST1H1B","url":"https://www.omim.org/entry/142711"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"bone marrow","ntpm":7.3},{"tissue":"lymphoid tissue","ntpm":1.9}],"url":"https://www.proteinatlas.org/search/H1-5"},"hgnc":{"alias_symbol":["H1b","H1s-3"],"prev_symbol":["H1F5","HIST1H1B"]},"alphafold":{"accession":"P16401","domains":[{"cath_id":"1.10.10.10","chopping":"42-109","consensus_level":"high","plddt":95.0107,"start":42,"end":109}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P16401","model_url":"https://alphafold.ebi.ac.uk/files/AF-P16401-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P16401-F1-predicted_aligned_error_v6.png","plddt_mean":63.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=H1-5","jax_strain_url":"https://www.jax.org/strain/search?query=H1-5"},"sequence":{"accession":"P16401","fasta_url":"https://rest.uniprot.org/uniprotkb/P16401.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P16401/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P16401"}},"corpus_meta":[{"pmid":"15192231","id":"PMC_15192231","title":"MSX1 cooperates with histone H1b for inhibition of transcription and myogenesis.","date":"2004","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/15192231","citation_count":195,"is_preprint":false},{"pmid":"23746450","id":"PMC_23746450","title":"The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells.","date":"2013","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/23746450","citation_count":103,"is_preprint":false},{"pmid":"22956909","id":"PMC_22956909","title":"Dynamic distribution of linker histone H1.5 in cellular differentiation.","date":"2012","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22956909","citation_count":68,"is_preprint":false},{"pmid":"9031620","id":"PMC_9031620","title":"Characterization of the H1.5 gene completes the set of human H1 subtype genes.","date":"1997","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/9031620","citation_count":48,"is_preprint":false},{"pmid":"19609548","id":"PMC_19609548","title":"Site-specifically phosphorylated forms of H1.5 and H1.2 localized at distinct regions of the nucleus are related to different processes during the cell cycle.","date":"2009","source":"Chromosoma","url":"https://pubmed.ncbi.nlm.nih.gov/19609548","citation_count":41,"is_preprint":false},{"pmid":"9079620","id":"PMC_9079620","title":"Histone H1b phosphorylation is dependent upon ongoing transcription and replication in normal and ras-transformed mouse fibroblasts.","date":"1997","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9079620","citation_count":39,"is_preprint":false},{"pmid":"19136008","id":"PMC_19136008","title":"M phase-specific phosphorylation of histone H1.5 at threonine 10 by GSK-3.","date":"2008","source":"Journal of molecular 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HIV-1.","date":"2004","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15610014","citation_count":19,"is_preprint":false},{"pmid":"28100789","id":"PMC_28100789","title":"Complex Evolutionary History of the Mammalian Histone H1.1-H1.5 Gene Family.","date":"2017","source":"Molecular biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/28100789","citation_count":19,"is_preprint":false},{"pmid":"26912777","id":"PMC_26912777","title":"Photobleaching studies reveal that a single amino acid polymorphism is responsible for the differential binding affinities of linker histone subtypes H1.1 and H1.5.","date":"2016","source":"Biology open","url":"https://pubmed.ncbi.nlm.nih.gov/26912777","citation_count":19,"is_preprint":false},{"pmid":"3115569","id":"PMC_3115569","title":"Reduced levels of histones H1o and H1b, and unaltered content of methylated DNA in rainbow trout hepatocellular carcinoma chromatin.","date":"1987","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/3115569","citation_count":18,"is_preprint":false},{"pmid":"31076740","id":"PMC_31076740","title":"Histone H1.5 binds over splice sites in chromatin and regulates alternative splicing.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31076740","citation_count":16,"is_preprint":false},{"pmid":"33214908","id":"PMC_33214908","title":"Linker histone H1.5 is an underestimated factor in differentiation and carcinogenesis.","date":"2020","source":"Environmental epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/33214908","citation_count":15,"is_preprint":false},{"pmid":"9182532","id":"PMC_9182532","title":"A mouse histone H1 variant, H1b, binds preferentially to a regulatory sequence within a mouse H3.2 replication-dependent histone gene.","date":"1997","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9182532","citation_count":13,"is_preprint":false},{"pmid":"21110323","id":"PMC_21110323","title":"Assaying pharmacodynamic endpoints with targeted therapy: flavopiridol and 17AAG induced dephosphorylation of histone H1.5 in acute myeloid leukemia.","date":"2010","source":"Proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/21110323","citation_count":13,"is_preprint":false},{"pmid":"34746019","id":"PMC_34746019","title":"HIST1H1B Promotes Basal-Like Breast Cancer Progression by Modulating CSF2 Expression.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34746019","citation_count":12,"is_preprint":false},{"pmid":"12601555","id":"PMC_12601555","title":"Isolation and characterization of a novel human NM23-H1B gene, a different transcript of NM23-H1.","date":"2003","source":"Journal of human 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presence.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/38530350","citation_count":5,"is_preprint":false},{"pmid":"20674357","id":"PMC_20674357","title":"Novel imidazobenzazepine derivatives as dual H1/5-HT2A antagonists for the treatment of sleep disorders.","date":"2010","source":"Bioorganic & medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/20674357","citation_count":5,"is_preprint":false},{"pmid":"39019868","id":"PMC_39019868","title":"Biochemical role of FOXM1-dependent histone linker H1B in human epidermal stem cells.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/39019868","citation_count":4,"is_preprint":false},{"pmid":"40568180","id":"PMC_40568180","title":"Linker Histone H1.5 Contributes to Centromere Integrity in Human Cells.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40568180","citation_count":1,"is_preprint":false},{"pmid":"19811742","id":"PMC_19811742","title":"[Preparation and identification of polyclonal antibody against protein H1b: the variant of major subunit of human ASGPR].","date":"2009","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/19811742","citation_count":1,"is_preprint":false},{"pmid":"41521667","id":"PMC_41521667","title":"Linker histone H1.5 contributes to centromere integrity.","date":"2026","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41521667","citation_count":0,"is_preprint":false},{"pmid":"16635329","id":"PMC_16635329","title":"[Study on mRNA expression of the human novel gene NM23-H1B in ovarian tumor].","date":"2006","source":"Zhonghua fu chan ke za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/16635329","citation_count":0,"is_preprint":false},{"pmid":"40739080","id":"PMC_40739080","title":"Development, Characterization, and in vitro Efficacy Evaluation of an Inhalable H1B Antimicrobial Peptide Formulation for Treating Non-Small Cell Lung Cancer.","date":"2025","source":"AAPS PharmSciTech","url":"https://pubmed.ncbi.nlm.nih.gov/40739080","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15963,"output_tokens":3901,"usd":0.053202,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11615,"output_tokens":4892,"usd":0.090188,"stage2_stop_reason":"end_turn"},"total_usd":0.14339,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"MSX1 physically interacts with histone H1b (H1-5 mouse ortholog) and together they bind to a key regulatory element of MyoD, inducing repressed chromatin and cooperating to inhibit skeletal muscle differentiation in cell culture and Xenopus animal caps.\",\n      \"method\": \"Physical interaction identified by co-immunoprecipitation/pulldown; chromatin binding demonstrated by ChIP; functional cooperation shown by cell culture and Xenopus animal cap assays\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, ChIP, and functional loss-of-function in two independent systems (cell culture and Xenopus)\",\n      \"pmids\": [\"15192231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"H1.5 binds genic and intergenic regions in differentiated human cells (but not embryonic stem cells), preferentially at membrane-related gene families; H1.5 binding is required for SIRT1 binding, H3K9me2 enrichment, and chromatin compaction. Depletion of H1.5 causes loss of SIRT1 and H3K9me2, increased chromatin accessibility, deregulation of gene expression, and decreased cell growth.\",\n      \"method\": \"ChIP-seq for H1.5 genomic distribution; siRNA-mediated knockdown with ChIP for SIRT1 and H3K9me2, chromatin accessibility assays, gene expression profiling, and cell growth assays\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (ChIP-seq, KD, histone mark analysis, chromatin accessibility) in a single rigorous study\",\n      \"pmids\": [\"22956909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"H1.5 undergoes site-specific phosphorylation at distinct residues during the cell cycle: Ser(17) and Ser(172) appear in interphase at DNA replication and transcription sites, while Thr(10) phosphorylation begins in prophase and peaks in metaphase on chromatin-bound H1.5, disappearing before chromatin decondensation. Different kinases are implicated at different sites (staurosporine sensitivity).\",\n      \"method\": \"Affinity-purified phosphosite-specific polyclonal antibodies; immunofluorescence in synchronized HeLa cells; kinase inhibitor (staurosporine) treatment; colocalization with replication/transcription markers\",\n      \"journal\": \"Chromosoma\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — specific antibody-based imaging in synchronized cells with inhibitor validation, single lab\",\n      \"pmids\": [\"19609548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"GSK-3 phosphorylates H1.5 at threonine 10 during M phase. This phosphorylation appears in prometaphase and disappears in telophase; the hyperphosphorylated form is mainly chromatin-bound in metaphase. GSK-3 inhibitors reduce Thr10 phosphorylation both in vitro and in vivo; CDK1/cyclin B and CDK5/p35 do not phosphorylate this site.\",\n      \"method\": \"In vitro kinase assays with GSK-3, CDK1/cyclin B, and CDK5/p35; immunofluorescence with phosphospecific antiserum in HeLa cells; GSK-3 inhibitor treatment in cells\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay identifying the writer, confirmed in vivo with inhibitors, negative controls for other kinases included\",\n      \"pmids\": [\"19136008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"H1b (H1-5 mouse ortholog) selectively binds the Omega regulatory element within the coding region of the replication-dependent H3.2 histone gene with ~100-fold higher affinity than the comparable sequence of the replication-independent H3.3 gene, suggesting a specific role in regulating replication-dependent histone gene expression.\",\n      \"method\": \"In vitro binding assays (gel mobility shift/footprinting) comparing H1b affinity for H3.2 vs H3.3 Omega sequences\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding assay with sequence specificity demonstrated, single lab\",\n      \"pmids\": [\"9182532\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Phosphorylation of H1b (H1-5 mouse ortholog) is dependent on ongoing transcription and replication: inhibition of transcription (actinomycin D, DRB) or replication (aphidicolin) markedly decreases pH1b levels, and phosphorylation is restored after removal of DRB. This suggests pH1b is associated with transcribing chromatin and that phosphorylation may facilitate chromatin decondensation for transcription and replication.\",\n      \"method\": \"Pharmacological inhibition of transcription and replication in normal and ras-transformed mouse fibroblasts; quantification of pH1b by Western blot/immunological methods\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological perturbation with functional readout, single lab, two inhibitors for transcription tested\",\n      \"pmids\": [\"9079620\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"H1.5 binds DNA over splice sites of short exons in human lung fibroblasts, and this binding correlates with inclusion of alternatively spliced exons. Depletion of H1.5 decreases exon inclusion and reduces RNA polymerase II levels over these exons, indicating H1.5 regulates alternative splicing through RNAP II stalling near 3' splice sites.\",\n      \"method\": \"ChIP-seq for H1.5 binding at splice sites; siRNA knockdown of H1.5; RT-PCR for exon inclusion; ChIP for RNAP II occupancy\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP-seq, functional knockdown, and RNAP II ChIP as orthogonal mechanistic methods in a single study\",\n      \"pmids\": [\"31076740\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Differences in chromatin-binding affinity between H1.1 (lower) and H1.5 (higher) were mapped by in vitro mutagenesis to a single amino acid polymorphism near the junction of the globular and C-terminal domains. Overexpression of H1.5 in density-arrested fibroblasts did not affect cell cycle progression after release.\",\n      \"method\": \"FRAP (fluorescence recovery after photobleaching) to measure exchange rates; in vitro mutagenesis; cell cycle analysis after H1 overexpression\",\n      \"journal\": \"Biology open\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro mutagenesis with FRAP readout, single lab study\",\n      \"pmids\": [\"26912777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"H1.5 (along with H1.2–H1.4) is depleted from CpG-dense regions and active regulatory regions in human lung fibroblasts, while it marks specific repressive domains, implicating H1.5 in three-dimensional genome organization.\",\n      \"method\": \"DamID (DNA adenine methyltransferase identification) genome-wide mapping of all five somatic H1 subtypes\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide DamID mapping, single lab, cross-subtype comparison\",\n      \"pmids\": [\"23746450\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Monoubiquitinated H1B is secreted from HRF+ CD4+ T cells resistant to HIV-1. Specific siRNA silencing of H1B in HRF+ cells reduced antiviral activity of supernatants by 96% and reversed the HIV-1 resistance phenotype, establishing H1B as a required cofactor for HRF-mediated antiviral protection.\",\n      \"method\": \"RNAi knockdown of H1B; Western blot with anti-H1 and anti-ubiquitin antibodies; antiviral activity assays on cell culture supernatants\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi knockdown with functional antiviral assay readout, single lab\",\n      \"pmids\": [\"15610014\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Ras-AKT signaling represses phosphorylation of H1.5 at Thr10 through MDM2-dependent degradation of GSK3, thereby promoting glioma cell growth and migration. Overexpression of H1.5-T10ph inhibits Ras-driven growth and migration, and H1.5-T10ph regulates transcription of Ras downstream genes (CYR61, IGFBP3, WNT16B, NT5E, GDF15, CARD16).\",\n      \"method\": \"Plasmid transfection of Ras/AKT constructs; Western blot for phospho-H1.5-T10 and phospho-AKT; MTT, soft-agar colony formation, transwell migration assays; qRT-PCR and ChIP assay for downstream gene regulation\",\n      \"journal\": \"Artificial cells, nanomedicine, and biotechnology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays and ChIP, single lab, pathway placement by epistasis\",\n      \"pmids\": [\"31307224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FOXM1 binds the H1B promoter region and regulates H1B expression in human epidermal stem cells. H1B in turn binds the promoter regions of differentiation-related genes and negatively regulates their expression, placing H1B downstream of FOXM1 in a pathway controlling self-renewal versus differentiation.\",\n      \"method\": \"Single-cell transcriptomics; ChIP assay (FOXM1 binding to H1B promoter; H1B binding to differentiation gene promoters); enforced FOXM1 expression experiments; analysis of H1B expression across clonal types\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and functional overexpression experiments, single lab\",\n      \"pmids\": [\"39019868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HIST1H1B (H1-5) upregulates CSF2 (colony-stimulating factor 2) expression by binding the CSF2 promoter in basal-like breast cancer cells, thereby promoting tumor growth and migration. Knockdown of HIST1H1B suppresses tumorigenicity.\",\n      \"method\": \"ChIP assay for H1B binding at CSF2 promoter; transwell, colony formation, and mammosphere assays; tumorigenesis assays; qRT-PCR\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP linking H1B to CSF2 promoter, knockdown with functional tumorigenesis readout, single lab\",\n      \"pmids\": [\"34746019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"H1.5 is universally enriched at the nuclear periphery and co-localizes with compacted DNA in all human cell lines examined. Knockdown of H1.5 (alone or combined) does not trigger global chromatin decompaction, whereas H1.2 knockdown does; the depletion of H1.5 causes variant-specific chromatin structure alterations.\",\n      \"method\": \"Super-resolution microscopy and immunofluorescence imaging of H1 variants; siRNA knockdown; chromatin structure assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct imaging with super-resolution and functional knockdown, single lab, multiple cell lines\",\n      \"pmids\": [\"38530350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"H1.5 directly interacts with CENP-A mononucleosomes in vitro and localizes to centromeres in human cells. ChIP confirms interaction between H1.5 and centromeric chromatin. Knockdown of H1.5 results in loss of centromeric α-satellite transcription, reduced loading of new CENP-A, altered kinetochore protein gene expression, and accumulation of mitotic defects.\",\n      \"method\": \"In vitro binding assays with CENP-A mononucleosomes; immunofluorescence localization; ChIP; siRNA knockdown with analysis of CENP-A loading, α-satellite transcription, and mitotic defects\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution, ChIP in vivo, and functional knockdown with multiple orthogonal readouts; peer-reviewed publication\",\n      \"pmids\": [\"41521667\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"H1-5 (H1.5/H1b) is a linker histone that compacts chromatin at the nuclear periphery and specific gene loci by interacting with CENP-A nucleosomes at centromeres (required for CENP-A loading and mitotic integrity), recruiting SIRT1 and H3K9me2 to repress defined gene families, binding splice-site DNA to slow RNA polymerase II and regulate alternative splicing, and cooperating with transcription factors such as MSX1 (to repress MyoD) and acting downstream of FOXM1 (to silence differentiation genes); its activity is modulated by cell-cycle-regulated, site-specific phosphorylation—with GSK-3 phosphorylating Thr10 in M phase and Ras-AKT-MDM2 suppressing this modification—as well as by monoubiquitination that enables its secretion as a cofactor in antiviral responses.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"H1-5 (H1.5/H1b) is a somatic linker histone that organizes higher-order chromatin structure and acts as a locus-specific transcriptional repressor in differentiated cells [#1, #13]. It is enriched at the nuclear periphery in association with compacted DNA, and in differentiated (but not embryonic stem) cells it binds defined genic and intergenic domains—preferentially membrane-related gene families—where its presence is required for recruitment of SIRT1, enrichment of repressive H3K9me2, and chromatin compaction; depletion increases chromatin accessibility, deregulates gene expression, and slows cell growth [#1, #13]. H1-5 directs gene silencing through cooperation with sequence-specific factors, repressing MyoD together with the homeoprotein MSX1 to block muscle differentiation [#0] and acting downstream of FOXM1 to bind and repress differentiation-gene promoters in epidermal stem cells, thereby balancing self-renewal against differentiation [#11]. Beyond steady-state chromatin, it binds DNA over short-exon splice sites and slows RNA polymerase II near 3' splice sites to promote exon inclusion, coupling chromatin to alternative splicing [#6], and it directly interacts with CENP-A nucleosomes at centromeres where it is required for α-satellite transcription, new CENP-A loading, and mitotic fidelity [#14]. H1-5 activity is regulated by cell-cycle, site-specific phosphorylation: GSK-3 phosphorylates Thr10 on chromatin-bound H1.5 from prometaphase to telophase, and Ras-AKT signaling suppresses this mark via MDM2-dependent GSK3 degradation to promote glioma growth [#3, #10]. In disease contexts it has been linked to oncogenic transcription, upregulating CSF2 in basal-like breast cancer to drive tumorigenicity [#12].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Established that the linker histone H1b has intrinsic DNA-sequence selectivity rather than acting only as a generic chromatin compactor, and that its phosphorylation tracks active genome processes.\",\n      \"evidence\": \"In vitro binding assays comparing affinity for H3.2 vs H3.3 Omega elements, and pharmacological inhibition of transcription/replication with pH1b quantification in mouse fibroblasts\",\n      \"pmids\": [\"9182532\", \"9079620\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vitro sequence preference not validated genome-wide\", \"Kinase responsible for transcription/replication-linked phosphorylation not identified\", \"Functional consequence of H3.2 gene binding in vivo untested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showed that H1-5 represses specific genes by partnering with a sequence-specific transcription factor, defining a targeted rather than purely structural role.\",\n      \"evidence\": \"Co-IP, ChIP, and functional differentiation assays of MSX1–H1b at the MyoD locus in cell culture and Xenopus animal caps\",\n      \"pmids\": [\"15192231\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MSX1 recruits H1b or vice versa unresolved\", \"Generality beyond MyoD unknown at the time\", \"No structural basis for the interaction\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Revealed an unexpected extracellular role: monoubiquitinated H1B is secreted and required for HRF-mediated antiviral protection, extending H1-5 function beyond chromatin.\",\n      \"evidence\": \"siRNA silencing of H1B in HRF+ CD4+ T cells with antiviral activity assays on supernatants and anti-ubiquitin Western blots\",\n      \"pmids\": [\"15610014\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of secretion and ubiquitination not defined\", \"Single-system observation not independently confirmed\", \"Molecular target of secreted H1B in antiviral activity unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined H1.5 as a phosphorylation-regulated histone with distinct interphase and mitotic phosphosites, linking specific modifications to replication, transcription, and mitotic chromatin states.\",\n      \"evidence\": \"Phosphosite-specific antibodies and immunofluorescence in synchronized HeLa cells with staurosporine and replication/transcription marker colocalization\",\n      \"pmids\": [\"19609548\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinases for Ser17/Ser172 not identified\", \"Functional consequence of each phosphosite not tested\", \"Antibody-based localization without orthogonal confirmation\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identified GSK-3 as the writer of the mitotic Thr10 mark, placing H1.5 phosphorylation under a defined kinase and excluding alternative mitotic kinases.\",\n      \"evidence\": \"In vitro kinase assays with GSK-3, CDK1/cyclinB, CDK5/p35 plus phosphospecific immunofluorescence and GSK-3 inhibition in HeLa cells\",\n      \"pmids\": [\"19136008\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream effect of Thr10ph on chromatin function not established here\", \"Upstream control of GSK-3 toward H1.5 unknown\", \"Whether Thr10ph alters DNA/nucleosome binding untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Provided the genome-wide mechanistic picture: H1.5 binding in differentiated cells nucleates a repressive SIRT1/H3K9me2 compaction module at specific gene families.\",\n      \"evidence\": \"ChIP-seq of H1.5 with siRNA knockdown and ChIP for SIRT1/H3K9me2, chromatin accessibility, expression and growth assays in human cells\",\n      \"pmids\": [\"22956909\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Order of recruitment of H1.5, SIRT1, H3K9me2 not resolved\", \"Why ESCs lack H1.5 binding unexplained\", \"Direct vs indirect dependence of SIRT1 on H1.5 not separated\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Mapped H1.5 within the broader linker-histone repertoire, showing depletion from active/CpG-dense regions and enrichment in repressive domains, implicating it in 3D genome organization.\",\n      \"evidence\": \"DamID genome-wide mapping of all five somatic H1 subtypes in human lung fibroblasts\",\n      \"pmids\": [\"23746450\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of repressive-domain marking not tested\", \"Subtype-specific contribution not isolated by perturbation\", \"Relationship to nuclear-periphery localization not directly linked\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Traced H1.5's higher chromatin-binding affinity to a single residue near the globular/C-terminal junction, providing a molecular determinant of variant-specific behavior.\",\n      \"evidence\": \"FRAP exchange-rate measurements with in vitro mutagenesis and cell-cycle analysis after overexpression\",\n      \"pmids\": [\"26912777\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Affinity difference not connected to a downstream function\", \"Overexpression showed no cell-cycle effect, leaving phenotype unclear\", \"Single-residue effect not tested in chromatin context genome-wide\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended H1.5 function to co-transcriptional RNA processing, showing it controls alternative splicing by stalling RNAP II at splice sites of short exons.\",\n      \"evidence\": \"ChIP-seq of H1.5 at splice sites, siRNA knockdown, RT-PCR for exon inclusion, and RNAP II ChIP in human lung fibroblasts\",\n      \"pmids\": [\"31076740\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which H1.5 stalls RNAP II not defined\", \"Whether splicing role depends on its repressive partners unknown\", \"Spliceosome interplay not characterized\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Placed H1.5-T10 phosphorylation in an oncogenic signaling axis, showing Ras-AKT-MDM2 suppresses the mark to relieve repression of Ras target genes and promote glioma growth.\",\n      \"evidence\": \"Ras/AKT transfection with phospho-H1.5-T10 Western blot, growth/migration assays, and ChIP/qRT-PCR for downstream genes\",\n      \"pmids\": [\"31307224\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding of H1.5-T10ph to target promoters vs indirect effect not separated\", \"GSK3 degradation mechanism by MDM2 not structurally defined\", \"Findings restricted to glioma model\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated a gene-activating, pro-tumorigenic role in breast cancer, contrasting with H1.5's repressive functions elsewhere.\",\n      \"evidence\": \"ChIP at CSF2 promoter, knockdown with colony/mammosphere/tumorigenesis assays in basal-like breast cancer cells\",\n      \"pmids\": [\"34746019\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How a linker histone activates CSF2 not mechanistically explained\", \"Cofactors at the CSF2 promoter not identified\", \"Context-dependence vs repressive role unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Positioned H1B in a FOXM1-driven self-renewal/differentiation circuit, showing it is a transcriptional effector repressing differentiation genes in epidermal stem cells.\",\n      \"evidence\": \"scRNA-seq, ChIP for FOXM1→H1B promoter and H1B→differentiation-gene promoters, and enforced FOXM1 expression\",\n      \"pmids\": [\"39019868\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether H1B repression uses the SIRT1/H3K9me2 module here untested\", \"Direct FOXM1–H1B regulatory step vs indirect not fully isolated\", \"In vivo requirement not established\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established universal nuclear-periphery enrichment and variant-specific, non-redundant chromatin roles distinguishing H1.5 from H1.2.\",\n      \"evidence\": \"Super-resolution imaging and siRNA knockdown of H1 variants across multiple human cell lines\",\n      \"pmids\": [\"38530350\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of variant-specific effects not defined\", \"Why H1.5 KD does not globally decompact unexplained\", \"Periphery-tethering mechanism unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a direct centromeric function: H1.5 binds CENP-A nucleosomes and is required for α-satellite transcription, CENP-A loading, and mitotic integrity.\",\n      \"evidence\": \"In vitro binding to CENP-A mononucleosomes, immunofluorescence, ChIP, and siRNA knockdown with CENP-A loading and mitotic-defect readouts\",\n      \"pmids\": [\"41521667\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of H1.5–CENP-A interaction not solved\", \"How H1.5 promotes α-satellite transcription mechanistically unclear\", \"Relationship to Thr10 mitotic phosphorylation not linked\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single linker histone reconciles opposing context-dependent outputs—peripheral compaction and repression, RNAP II stalling for splicing, centromeric CENP-A support, and gene activation in cancer—remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model linking phosphorylation/ubiquitination state to functional switching\", \"Direct interactome at distinct loci not comprehensively defined\", \"Structural mechanism of CENP-A and splice-site DNA recognition unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [4, 6, 14]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 1, 11, 12]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [1, 13]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [14]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2, 13]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [3, 13]},\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [13]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [1, 8, 13]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 11, 12]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [2, 3, 14]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"MSX1\", \"SIRT1\", \"CENP-A\", \"FOXM1\", \"GSK3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}