KMT5A Gene

Name lysine methyltransferase 5A
Description The protein encoded by this gene is a protein-lysine N-methyltransferase that can monomethylate Lys-20 of histone H4 to effect transcriptional repression of some genes. The encoded protein is required for cell proliferation and plays a role in chromatin condensation. [provided by RefSeq, May 2016]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n KMT5A, also known as PR‐Set7 or Set8, is the sole enzyme that monomethylates histone H4 at lysine 20 (H4K20me1) and is essential for multiple aspects of chromatin regulation. Its activity establishes a chromatin state critical for proper cell cycle progression by promoting chromatin compaction, ensuring proper mitotic chromosome condensation, and facilitating replication licensing through the efficient assembly of pre‐replication complexes at replication origins."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": " During S phase, regulated proteolysis of KMT5A via a PCNA‐ and CRL4(Cdt2)–dependent mechanism ensures that H4K20me1 accumulation remains transient, thereby protecting against replication stress and aberrant chromatin compaction."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}, {"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n Beyond its role in DNA replication and mitosis, KMT5A exerts important functions in the DNA damage response and cell cycle checkpoint control. It modulates the tumor suppressor p53 by catalyzing specific methylation events that repress or fine‐tune p53‐mediated transcription, thereby influencing the balance between cell cycle arrest and apoptosis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " In addition, KMT5A’s activity is indispensable during embryonic development; loss of its catalytic function causes early embryonic lethality and severe replication defects."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n The structural basis for substrate recognition and catalytic specificity has been elucidated, revealing how KMT5A selectively deposits the monomethyl mark on H4K20."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": " Furthermore, KMT5A-dependent H4K20me1 participates in transcriptional regulation during differentiation processes such as adipogenesis and even in the modulation of Wnt signaling, where it activates key transcription factors."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": " Notably, KMT5A also methylates nonhistone substrates such as PCNA, enhancing its stability and promoting interactions with essential replication factors like FEN1."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "11"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, KMT5A is a central regulator of chromatin dynamics that integrates signals from DNA replication, repair, and transcription to maintain genomic stability. Its tightly controlled activity throughout the cell cycle ensures proper chromosome condensation and cell cycle progression, while its dysregulation is linked to developmental defects and tumorigenesis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "12", "end_ref": "14"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Mathieu Tardat, Julien Brustel, Olivier Kirsh, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Regulation of the histone H4 monomethylase PR-Set7 by CRL4(Cdt2)-mediated PCNA-dependent degradation during DNA damage."}]}, {"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.2010.10.011"}], "href": "https://doi.org/10.1016/j.molcel.2010.10.011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21035370"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21035370"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Richard C Centore, Courtney G Havens, Amity L Manning, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CRL4(Cdt2)-mediated destruction of the histone methyltransferase Set8 prevents premature chromatin compaction in S phase."}]}, {"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.2010.09.015"}], "href": "https://doi.org/10.1016/j.molcel.2010.09.015"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20932472"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20932472"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Xiaobing Shi, Ioulia Kachirskaia, Hiroshi Yamaguchi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Modulation of p53 function by SET8-mediated methylation at lysine 382."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2007.07.012"}], "href": "https://doi.org/10.1016/j.molcel.2007.07.012"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17707234"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17707234"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Hisanobu Oda, Ikuhiro Okamoto, Niall Murphy, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Monomethylation of histone H4-lysine 20 is involved in chromosome structure and stability and is essential for mouse development."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.01768-08"}], "href": "https://doi.org/10.1128/MCB.01768-08"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19223465"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19223465"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Stine Jørgensen, Ingegerd Elvers, Morten Beck Trelle, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The histone methyltransferase SET8 is required for S-phase progression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biol (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1083/jcb.200706150"}], "href": "https://doi.org/10.1083/jcb.200706150"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18166648"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18166648"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Jean-François Couture, Evys Collazo, Joseph S Brunzelle, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.1318405"}], "href": "https://doi.org/10.1101/gad.1318405"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15933070"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15933070"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Ken-ichi Wakabayashi, Masashi Okamura, Shuichi Tsutsumi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The peroxisome proliferator-activated receptor gamma/retinoid X receptor alpha heterodimer targets the histone modification enzyme PR-Set7/Setd8 gene and regulates adipogenesis through a positive feedback loop."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.01856-08"}], "href": "https://doi.org/10.1128/MCB.01856-08"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19414603"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19414603"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Zhenfei Li, Fen Nie, Sheng Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1009353108"}], "href": "https://doi.org/10.1073/pnas.1009353108"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21282610"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21282610"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Masashi Takawa, Hyun-Soo Cho, Shinya Hayami, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Histone lysine methyltransferase SETD8 promotes carcinogenesis by deregulating PCNA expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Res (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1158/0008-5472.CAN-11-3701"}], "href": "https://doi.org/10.1158/0008-5472.CAN-11-3701"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22556262"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22556262"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Lourdes Serrano, Paloma Martínez-Redondo, Anna Marazuela-Duque, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The tumor suppressor SirT2 regulates cell cycle progression and genome stability by modulating the mitotic deposition of H4K20 methylation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.211342.112"}], "href": "https://doi.org/10.1101/gad.211342.112"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23468428"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23468428"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "Fen Yang, Luyang Sun, Qian Li, et al. "}, {"type": "b", "children": [{"type": "t", "text": "SET8 promotes epithelial-mesenchymal transition and confers TWIST dual transcriptional activities."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/emboj.2011.364"}], "href": "https://doi.org/10.1038/emboj.2011.364"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21983900"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21983900"}]}, {"type": "r", "ref": 14, "children": [{"type": "t", "text": "N Kalakonda, W Fischle, P Boccuni, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oncogene (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/onc.2008.67"}], "href": "https://doi.org/10.1038/onc.2008.67"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18408754"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18408754"}]}]}]}
NCBI Gene ID 387893
API
Download Associations
Predicted Functions View KMT5A's ARCHS4 Predicted Functions.
Co-expressed Genes View KMT5A's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View KMT5A's ARCHS4 Predicted Functions.

Functional Associations

KMT5A has 2,772 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 45 datasets.

Click the + buttons to view associations for KMT5A 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 KMT5A 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 KMT5A gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CCLE Cell Line Proteomics Cell lines associated with KMT5A protein from the CCLE Cell Line Proteomics dataset.
CellMarker Gene-Cell Type Associations cell types associated with KMT5A gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of KMT5A 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 KMT5A gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing KMT5A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 cellular components containing KMT5A 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 KMT5A 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 KMT5A protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
DGIdb Drug Targets 2026 interacting drugs for KMT5A protein from the DGIdb Drug Targets 2026 dataset.
DISEASES Experimental Gene-Disease Association Evidence Scores 2025 diseases associated with KMT5A 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 KMT5A 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 KMT5A gene from the curated GO Biological Process Annotations 2023 dataset.
GO Biological Process Annotations 2025 biological processes involving KMT5A gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2023 cellular components containing KMT5A protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Cellular Component Annotations 2025 cellular components containing KMT5A protein from the curated GO Cellular Component Annotations 2025 dataset.
GO Molecular Function Annotations 2023 molecular functions performed by KMT5A gene from the curated GO Molecular Function Annotations 2023 dataset.
GO Molecular Function Annotations 2025 molecular functions performed by KMT5A gene from the curated GO Molecular Function Annotations 2025 dataset.
GTEx eQTL 2025 SNPs regulating expression of KMT5A gene from the GTEx eQTL 2025 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of KMT5A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with KMT5A gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of KMT5A 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 KMT5A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset.
KEGG Pathways 2026 pathways involving KMT5A protein from the KEGG Pathways 2026 dataset.
Kinase Library Tyrosine Kinome Atlas kinases that phosphorylate KMT5A protein from the Kinase Library Tyrosine Kinome Atlas dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of KMT5A gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
LINCS L1000 CMAP CRISPR Knockout Consensus Signatures gene perturbations changing expression of KMT5A gene from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset.
MGI Mouse Phenotype Associations 2023 phenotypes of transgenic mice caused by KMT5A gene mutations from the MGI Mouse Phenotype Associations 2023 dataset.
MoTrPAC Rat Endurance Exercise Training tissue samples with high or low expression of KMT5A gene relative to other tissue samples from the MoTrPAC Rat Endurance Exercise Training dataset.
MW Enzyme Metabolite Associations interacting metabolites for KMT5A protein from the MW Gene Metabolite Associations dataset.
NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles drug perturbations changing expression of KMT5A gene from the NIBR DRUG-seq U2OS MoA Box dataset.
PFOCR Pathway Figure Associations 2023 pathways involving KMT5A protein from the PFOCR Pathway Figure Associations 2023 dataset.
PFOCR Pathway Figure Associations 2024 pathways involving KMT5A protein from the Wikipathways PFOCR 2024 dataset.
Reactome Pathways 2024 pathways involving KMT5A protein from the Reactome Pathways 2024 dataset.
Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of KMT5A gene from the Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of KMT5A gene from the Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of KMT5A gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of KMT5A gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of KMT5A gene from the RummaGEO Gene Perturbation Signatures dataset.
Sci-Plex Drug Perturbation Signatures drug perturbations changing expression of KMT5A gene from the Sci-Plex Drug Perturbation Signatures dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of KMT5A 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 KMT5A 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 KMT5A protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.
WikiPathways Pathways 2024 pathways involving KMT5A protein from the WikiPathways Pathways 2024 dataset.