NELFE Gene

HGNC Family	RNA binding motif containing (RBM)
Name	negative elongation factor complex member E
Description	The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. [provided by RefSeq, Jul 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nNELFE, a key subunit of the four‐protein Negative Elongation Factor complex, plays a central role in mediating RNA polymerase II pausing during early transcription elongation. Studies reconstituting the DSIF/NELF complex demonstrated that the integrity of all subunits is required for its function, and mutations in critical regions of NELF‐E’s RNA recognition motif impair its ability to induce polymerase pausing, as observed in the regulation of immediate‐early genes such as junB. \n(«"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "»)"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditional work has revealed that beyond its canonical role in pausing transcription, NELFE participates in co‐transcriptional processes. It interacts with the nuclear cap binding complex to regulate the 3′‐end processing of replication‐dependent histone mRNAs, ensuring accurate mRNA maturation and preventing premature polyadenylation. Structural and biochemical investigations have mapped multiple RNA‐binding surfaces on the NELF core—especially within the NELF‐E subunit—highlighting conformational changes on RNA binding (for example, to elements such as those present in the HIV TAR RNA) and distinct subcellular localizations that suggest additional roles in RNA metabolism. \n(«"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": "»)"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn the context of viral gene regulation, NELFE-mediated pausing is exploited by viruses to control latent versus productive transcription. In models of herpesvirus and HIV latency, NELFE stabilizes RNA polymerase II in a paused state near promoter-proximal regions, preventing full-length transcript production. Depletion of NELF‐E has been shown to release this block, thereby enhancing viral gene expression. \n(«"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "10"}]}, {"type": "t", "text": "»)"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nRecent evidence further implicates aberrant NELFE function in human cancer. In pancreatic and gastric carcinomas, elevated levels of NELFE correlate with enhanced tumorigenesis through activation of the Wnt/β‐catenin signaling pathway—mediated, in part, via destabilization of specific tumor suppressor mRNAs—and contribute to metastatic progression. Moreover, NELFE has been linked to the cellular DNA damage response, as it facilitates homologous recombination repair through interactions with the breast cancer susceptibility factor BRCA1. \n(«"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "11"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "12"}]}, {"type": "t", "text": "», «"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "13"}]}, {"type": "t", "text": "»)"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Yuki Yamaguchi, Naoto Inukai, Takashi Narita, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.22.9.2918-2927.2002"}], "href": "https://doi.org/10.1128/MCB.22.9.2918-2927.2002"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "11940650"}], "href": "https://pubmed.ncbi.nlm.nih.gov/11940650"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Takashi Narita, Yuki Yamaguchi, Keiichi Yano, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.23.6.1863-1873.2003"}], "href": "https://doi.org/10.1128/MCB.23.6.1863-1873.2003"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12612062"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12612062"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Masatoshi Aida, Yexi Chen, Koichi Nakajima, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.02366-05"}], "href": "https://doi.org/10.1128/MCB.02366-05"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16880520"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16880520"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Takashi Narita, Tetsu M C Yung, Junichi Yamamoto, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs."}]}, {"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.2007.04.011"}], "href": "https://doi.org/10.1016/j.molcel.2007.04.011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17499042"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17499042"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Jampani Nageswara Rao, Kristian Schweimer, Sabine Wenzel, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochemistry (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1021/bi702429m"}], "href": "https://doi.org/10.1021/bi702429m"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18303858"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18303858"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Tetsu M C Yung, Takashi Narita, Toshiharu Komori, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Cellular dynamics of the negative transcription elongation factor NELF."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Exp Cell Res (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.yexcr.2009.02.013"}], "href": "https://doi.org/10.1016/j.yexcr.2009.02.013"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19245807"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19245807"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "John M Pagano, Hojoong Kwak, Colin T Waters, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS Genet (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pgen.1004090"}], "href": "https://doi.org/10.1371/journal.pgen.1004090"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24453987"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24453987"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Seychelle M Vos, David Pöllmann, Livia Caizzi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Architecture and RNA binding of the human negative elongation factor."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Elife (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.7554/eLife.14981"}], "href": "https://doi.org/10.7554/eLife.14981"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27282391"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27282391"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Arno Reich, Christopher Spering, Karen Gertz, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Fas/CD95 regulatory protein Faim2 is neuroprotective after transient brain ischemia."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Neurosci (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1523/JNEUROSCI.2188-10.2011"}], "href": "https://doi.org/10.1523/JNEUROSCI.2188-10.2011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21209208"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21209208"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Julie K Jadlowsky, Julian Y Wong, Amy C Graham, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.01013-13"}], "href": "https://doi.org/10.1128/MCB.01013-13"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24636995"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24636995"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Lili Han, Ying Zan, Chen Huang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NELFE promoted pancreatic cancer metastasis and the epithelial‑to‑mesenchymal transition by decreasing the stabilization of NDRG2 mRNA."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Oncol (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3892/ijo.2019.4890"}], "href": "https://doi.org/10.3892/ijo.2019.4890"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31638184"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31638184"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Laila A Bishara, Feras E Machour, Samah W Awwad, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NELF complex fosters BRCA1 and RAD51 recruitment to DNA damage sites and modulates sensitivity to PARP inhibition."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "DNA Repair (Amst) (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.dnarep.2020.103025"}], "href": "https://doi.org/10.1016/j.dnarep.2020.103025"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33248388"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33248388"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "Shijun Yu, Li Li, Hui Cai, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Overexpression of NELFE contributes to gastric cancer progression via Wnt/β-catenin signaling-mediated activation of CSNK2B expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Exp Clin Cancer Res (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s13046-021-01848-3"}], "href": "https://doi.org/10.1186/s13046-021-01848-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33526068"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33526068"}]}]}]}
Synonyms	RDBP, D6S45, NELF-E
Proteins	NELFE_HUMAN
NCBI Gene ID	7936
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

NELFE has 5,613 functional associations with biological entities spanning 7 categories (molecular profile, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 120 datasets.

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

If available, associations are ranked by standardized value

Harmonizome 3.0

NELFE 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 NELFE 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 NELFE 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 NELFE 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 NELFE 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 NELFE 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 NELFE 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 NELFE 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 NELFE 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 NELFE 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 NELFE gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of NELFE 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 NELFE gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with NELFE 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 NELFE gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of NELFE 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 NELFE 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 NELFE 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 NELFE gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing NELFE protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing NELFE protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with NELFE 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 NELFE protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing NELFE protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of NELFE gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with NELFE gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with NELFE gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with NELFE gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with NELFE gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with NELFE gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with NELFE 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 NELFE 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 NELFE 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 NELFE gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with NELFE 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 NELFE 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 NELFE gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of NELFE 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 NELFE from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with NELFE gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with NELFE gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.