MEPCE Gene

Name	methylphosphate capping enzyme
Description	Enables 7SK snRNA binding activity and RNA 5'-gamma-phosphate methyltransferase activity. Involved in RNA modification; positive regulation of protein localization to Cajal body; and positive regulation of snRNA transcription by RNA polymerase II. Located in nucleus. Part of 7SK snRNP. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nMEPCE is a specialized methylphosphate capping enzyme that, unlike the conventional capping enzyme involved in pre‐mRNA processing"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ", uniquely methylates and stabilizes the 7SK small nuclear RNA. This modification is essential for the assembly and function of the 7SK snRNP complex, which also includes proteins such as LARP7 and HEXIM1."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " In this complex, 7SK snRNP plays a dual role by regulating RNA polymerase II transcription elongation—not only by sequestering and thereby restraining the activity of positive transcription elongation factor b (P‑TEFb) during mRNA synthesis but also by facilitating the production of spliceosomal snRNA and small nucleolar RNA."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its RNA methyltransferase activity, MEPCE exhibits context‐dependent functionalities. Its ability to bind directly to the histone H4 tail on chromatin"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "indicates a switch from an RNA‐capping to a transcriptional activator role—promoting P‑TEFb function at genes critical to cellular identity. Moreover, studies analyzing the dynamics of the 7SK snRNP components reveal that the intricate network of protein–RNA interactions (including those involving HEXIM1) influences molecular diffusion and transcriptional regulation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " In cancer contexts, the integrity of these processes is vital: depletion of MEPCE in BRCA1‐deficient cells leads to aberrant promoter–proximal pausing, R‑loop accumulation, and replication stress"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": ", while in hepatocellular carcinoma, a regulatory axis involving miR‑1338 and MEPCE has been shown to modulate cell migration and invasion."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn addition to its roles in transcription regulation and genomic stability, MEPCE contributes to the maturation of non‐coding RNAs beyond 7SK. Specifically, it participates in the early processing of human telomerase RNA (hTR) in concert with LARP7; perturbation of this function disrupts proper hTR conversion and cytoplasmic accumulation, culminating in telomere shortening."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Syuzo Kaneko, Chun Chu, Aaron J Shatkin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Human capping enzyme promotes formation of transcriptional R loops in vitro."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.0708866104"}], "href": "https://doi.org/10.1073/pnas.0708866104"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17978174"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17978174"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Denise Martinez-Zapien, Jean-Michel Saliou, Xiao Han, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Intermolecular recognition of the non-coding RNA 7SK and HEXIM protein in perspective."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochimie (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.biochi.2015.03.020"}], "href": "https://doi.org/10.1016/j.biochi.2015.03.020"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25863285"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25863285"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Sylvain Egloff, Patrice Vitali, Michael Tellier, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.15252/embj.201695740"}], "href": "https://doi.org/10.15252/embj.201695740"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28254838"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28254838"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Samantha B Shelton, Nakul M Shah, Nathan S Abell, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Crosstalk between the RNA Methylation and Histone-Binding Activities of MePCE Regulates P-TEFb Activation on Chromatin."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Rep (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.celrep.2018.01.028"}], "href": "https://doi.org/10.1016/j.celrep.2018.01.028"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29425494"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29425494"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Alessandro Furlan, Mariano Gonzalez-Pisfil, Aymeric Leray, et al. "}, {"type": "b", "children": [{"type": "t", "text": "HEXIM1 Diffusion in the Nucleus Is Regulated by Its Interactions with Both 7SK and P-TEFb."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biophys J (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bpj.2019.09.019"}], "href": "https://doi.org/10.1016/j.bpj.2019.09.019"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31590891"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31590891"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Parasvi S Patel, Arash Algouneh, Rehna Krishnan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Excessive transcription-replication conflicts are a vulnerability of BRCA1-mutant cancers."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkad172"}], "href": "https://doi.org/10.1093/nar/gkad172"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36928661"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36928661"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Bin Zhang, Zhiyi Liu, Jin Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Long non‑coding RNA ST8SIA6‑AS1 promotes the migration and invasion of hypoxia‑treated hepatocellular carcinoma cells through the miR‑338/MEPCE axis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oncol Rep (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3892/or.2020.7864"}], "href": "https://doi.org/10.3892/or.2020.7864"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33416148"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33416148"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Tsai-Ling Kao, Yu-Cheng Huang, Yi-Hsuan Chen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "LARP3, LARP7, and MePCE are involved in the early stage of human telomerase RNA biogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-024-50422-w"}], "href": "https://doi.org/10.1038/s41467-024-50422-w"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "39009594"}], "href": "https://pubmed.ncbi.nlm.nih.gov/39009594"}]}]}]}
Synonyms	BCDIN3
Proteins	MEPCE_HUMAN
NCBI Gene ID	56257
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

MEPCE has 6,655 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 117 datasets.

Click the + buttons to view associations for MEPCE from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

MEPCE Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of MEPCE gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of MEPCE gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of MEPCE gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of MEPCE gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of MEPCE gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of MEPCE gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of MEPCE gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of MEPCE gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of MEPCE gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of MEPCE gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of MEPCE gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of MEPCE gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with MEPCE protein from the CCLE Cell Line Proteomics dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of MEPCE gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of MEPCE gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of MEPCE gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing MEPCE protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of MEPCE gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing MEPCE protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing MEPCE protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing MEPCE 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	cellular components co-occuring with MEPCE protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with MEPCE protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of MEPCE gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with MEPCE gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with MEPCE gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with MEPCE gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of MEPCE protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with MEPCE gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with MEPCE gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with MEPCE gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with MEPCE gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with MEPCE gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at MEPCE gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of MEPCE gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of MEPCE gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing MEPCE from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of MEPCE gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with MEPCE gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing MEPCE from the GeneSigDB Published Gene Signatures dataset.