H1-0 Gene

Name H1.0 linker histone
Description Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-independent histone that is a member of the histone H1 family. [provided by RefSeq, Oct 2015]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Linker histone H1–0 plays a central architectural role in modulating chromatin structure and, as a consequence, gene expression. Most studies indicate that H1–0 binding to nucleosomes helps establish a more compact chromatin conformation, thereby generally restricting access of the transcription machinery and dampening transcriptional noise. However, its function is tightly regulated by a variety of post‐translational modifications and protein–protein interactions that alter its affinity for chromatin.\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n For example, lysyl oxidase (LO) mediates oxidation of lysine residues in not only extracellular substrates like collagen and elastin but also in basic proteins such as histone H1, a modification that may contribute to altering its electrostatic interactions with DNA and its role in chromatin compaction."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " In addition, during transcriptional activation events such as those following topoisomerase IIβ–induced DNA breaks, an exchange event between histone H1 and high-mobility group B proteins is observed, implicating H1 displacement as a key step in remodeling chromatin to permit transcriptional changes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In neuronal cells, a delicate balance exists between repressive and activating chromatin marks. For instance, deficiency in methyl-CpG–binding protein MeCP2 results in global changes in chromatin structure, including a doubling in the abundance of histone H1, suggesting that an excess of H1 may contribute to improper chromatin compaction and dysregulated gene expression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Moreover, a reciprocal interplay has been observed between poly(ADP-ribose) polymerase-1 (PARP-1) and histone H1 at RNA polymerase II–transcribed promoters; while PARP-1 binding is enriched at active promoters, histone H1 is depleted. PARP-1 acts to evict or prevent the binding of H1, thereby promoting a more open and transcriptionally permissive chromatin state."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Post‐translational modifications also modulate H1 function. Citrullination of histone H1 by peptidylarginine deiminase 4 (PADI4) leads to its displacement from chromatin, resulting in global decondensation that is important for maintaining pluripotency and facilitating efficient cellular reprogramming."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " Furthermore, distinct histone-modifying complexes can target linker histone H1 for methylation. For example, complexes containing EZH2 and alternative isoforms of Eed selectively methylate histone H1 at lysine 26, a modification that likely influences its ability to compact chromatin."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Finally, PARP-1 is also implicated in the active exclusion of H1 from promoter regions. By preventing the association of H1 at these loci, PARP-1 facilitates an open chromatin environment that supports the loading of the RNA polymerase II machinery and efficient transcription initiation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Collectively, these studies underscore that H1–0 is not merely a passive linker but rather a dynamic regulator of chromatin architecture. Its activity is finely tuned by modifications—such as oxidation, methylation, and citrullination—and by its interplay with chromatin remodelers, which together influence processes ranging from differentiation and proliferation to the response of cells to DNA damage.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Herbert M Kagan, Wande Li "}, {"type": "b", "children": [{"type": "t", "text": "Lysyl oxidase: properties, specificity, and biological roles inside and outside of the cell."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biochem (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcb.10413"}], "href": "https://doi.org/10.1002/jcb.10413"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12577300"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12577300"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Bong-Gun Ju, Victoria V Lunyak, Valentina Perissi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1127196"}], "href": "https://doi.org/10.1126/science.1127196"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16794079"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16794079"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Peter J Skene, Robert S Illingworth, Shaun Webb, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2010.01.030"}], "href": "https://doi.org/10.1016/j.molcel.2010.01.030"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20188665"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20188665"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Raga Krishnakumar, Matthew J Gamble, Kristine M Frizzell, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1149250"}], "href": "https://doi.org/10.1126/science.1149250"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18258916"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18258916"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Maria A Christophorou, Gonçalo Castelo-Branco, Richard P Halley-Stott, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Citrullination regulates pluripotency and histone H1 binding to chromatin."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature12942"}], "href": "https://doi.org/10.1038/nature12942"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24463520"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24463520"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Andrei Kuzmichev, Thomas Jenuwein, Paul Tempst, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/s1097-2765(04)00185-6"}], "href": "https://doi.org/10.1016/s1097-2765(04"}, {"type": "t", "text": "00185-6) PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15099518"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15099518"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Raga Krishnakumar, W Lee Kraus "}, {"type": "b", "children": [{"type": "t", "text": "PARP-1 regulates chromatin structure and transcription through a KDM5B-dependent pathway."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2010.08.014"}], "href": "https://doi.org/10.1016/j.molcel.2010.08.014"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20832725"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20832725"}]}]}]}
NCBI Gene ID 3005
API
Download Associations
Predicted Functions View H1-0's ARCHS4 Predicted Functions.
Co-expressed Genes View H1-0's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View H1-0's ARCHS4 Predicted Functions.

Functional Associations

H1-0 has 9,434 functional associations with biological entities spanning 6 categories (chemical, functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 40 datasets.

Click the + buttons to view associations for H1-0 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles tissue samples with high or low expression of H1-0 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
Carcinogenome Chemical Perturbation Carcinogenicity Signatures small molecule perturbations changing expression of H1-0 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CCLE Cell Line Proteomics Cell lines associated with H1-0 protein from the CCLE Cell Line Proteomics dataset.
CellMarker Gene-Cell Type Associations cell types associated with H1-0 gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of H1-0 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
CM4AI KOLF21J CRISPRi Gene Perturbation Atlas gene perturbations changing expression of H1-0 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing H1-0 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 cellular components containing H1-0 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 cellular components co-occuring with H1-0 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
DeepCoverMOA Drug Mechanisms of Action small molecule perturbations with high or low expression of H1-0 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
DepMap CRISPR Gene Dependency cell lines with fitness changed by H1-0 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
DISEASES Experimental Gene-Disease Association Evidence Scores 2025 diseases associated with H1-0 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 diseases co-occuring with H1-0 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
GO Biological Process Annotations 2023 biological processes involving H1-0 gene from the curated GO Biological Process Annotations 2023 dataset.
GO Biological Process Annotations 2025 biological processes involving H1-0 gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2023 cellular components containing H1-0 protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Cellular Component Annotations 2025 cellular components containing H1-0 protein from the curated GO Cellular Component Annotations 2025 dataset.
GO Molecular Function Annotations 2023 molecular functions performed by H1-0 gene from the curated GO Molecular Function Annotations 2023 dataset.
GO Molecular Function Annotations 2025 molecular functions performed by H1-0 gene from the curated GO Molecular Function Annotations 2025 dataset.
GTEx eQTL 2025 SNPs regulating expression of H1-0 gene from the GTEx eQTL 2025 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of H1-0 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GTEx Tissue-Specific Aging Signatures tissue samples with high or low expression of H1-0 gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with H1-0 gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
IMPC Knockout Mouse Phenotypes phenotypes of mice caused by H1-0 gene knockout from the IMPC Knockout Mouse Phenotypes dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of H1-0 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
JASPAR Predicted Mouse Transcription Factor Targets 2025 transcription factors regulating expression of H1-0 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of H1-0 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
LINCS L1000 CMAP CRISPR Knockout Consensus Signatures gene perturbations changing expression of H1-0 gene from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset.
MGI Mouse Phenotype Associations 2023 phenotypes of transgenic mice caused by H1-0 gene mutations from the MGI Mouse Phenotype Associations 2023 dataset.
PFOCR Pathway Figure Associations 2023 pathways involving H1-0 protein from the PFOCR Pathway Figure Associations 2023 dataset.
PFOCR Pathway Figure Associations 2024 pathways involving H1-0 protein from the Wikipathways PFOCR 2024 dataset.
Reactome Pathways 2024 pathways involving H1-0 protein from the Reactome Pathways 2024 dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of H1-0 gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of H1-0 gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of H1-0 gene from the RummaGEO Gene Perturbation Signatures dataset.
Sci-Plex Drug Perturbation Signatures drug perturbations changing expression of H1-0 gene from the Sci-Plex Drug Perturbation Signatures dataset.
Tahoe Therapeutics Tahoe 100M Perturbation Atlas drug perturbations changing expression of H1-0 gene from the Tahoe Therapeutics Tahoe 100M Perturbation Atlas dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of H1-0 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 tissues with high expression of H1-0 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 tissues co-occuring with H1-0 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.