Alternative titles; symbols
HGNC Approved Gene Symbol: NELFE
Cytogenetic location: 6p21.33 Genomic coordinates (GRCh38) : 6:31,952,087-31,958,971 (from NCBI)
NELFE is a subunit of negative elongation factor (NELF), which also includes NELFA (606026), NELFB (611180), and either NELFC or NELFD (NELFCD; 605297). NELF acts with DRB sensitivity-inducing factor (DSIF), a heterodimer of SPT4 (SUPT4H1; 603555) and SPT5 (SUPT5H; 602102), to cause transcriptional pausing of RNA polymerase II (see 180660) (Narita et al., 2003).
Levi-Strauss et al. (1988) identified a novel gene that was transcribed in all tissues tested. The gene was found in the course of a search for undetected genes in the region of class III genes. From the nucleotide sequence derived from liver cDNA clones, it was predicted that this single-copy gene encodes a 42-kD polypeptide. The gene displayed striking hallmarks of natural selection. It was expressed at very low levels in a number of different cell types, thereby indicating that it may encode a housekeeping protein. The absence of a typical leader peptide from the deduced amino acid sequence may suggest that the protein is not destined to penetrate the endoplasmic reticulum and therefore its potential N-linked glycosylation site may not be used. The strong interspecies conservation of the nucleotide sequence and the even more rigidly preserved dipeptide repeat element, as well as the widespread expression of the gene, provide strong evidence that the protein subserves a fundamental and probably phylogenetically ancient function. For want of a better name, the authors referred to the gene as RD, the acronym of the most common dipeptide repeat; R and D are the single letter symbols for arginine and aspartic acid, respectively. In the central portion of the RD protein there is a 58-amino acid segment that consists almost entirely of alternating basic and acidic amino acids; there are 20 repeats of the sequence arg-asp. The only other protein known to contain extensive tracts of alternating arg-asp residues is the human U1 70K snRNP protein (180740), which specifically binds U1 snRNA. The RD protein contains the so-called RNP consensus sequence that is present in many different nuclear RNA-binding proteins, suggesting that the RD protein is a nucleic acid-binding protein. The sequence showed a very peculiar core region (centered on, but not limited to, nucleotides 725-880) containing about 8 imperfect repeats of approximately 15 nucleotides. This part of the mRNA encodes, in its most likely translation frame, a stretch of 52 amino acids composed exclusively of the perfect and monotonous reiteration of a dipeptide made of a basic residue (arginine or lysine) next to an acidic one (aspartic acid or glutamic acid). The strong conservation of the dipeptide residues stands in sharp contrast to the poor conservation of their codons, thus implying that the periodicity cannot be entirely accounted for by trivial rounds of recent duplications. Indeed, the multiplicity of codons specifying the most common dipeptide, arg-asp, and the presence of other combinations of amino acids such as arg-glu, lys-glu, and lys-asp imply the accumulation of multiple mutations which, even when occurring in the first base of the triplets, rigorously respect the charge periodicity of the structure by specifying the same or an isofunctional amino acid. Thus a strong selective pressure must have been responsible for the conservation of the unusual repeated motif. Surowy et al. (1988) isolated and sequenced cDNAs encoding RD RNA-binding protein.
Speiser and White (1989) stated that the RD gene was known earlier as D6S45. It encodes a protein predicted to contain 371 amino acids with a molecular weight of 41,000. The high degree of homology between the human and murine genes indicates functional importance for this conserved gene.
By Northern blot analysis, Narita et al. (2003) detected a major 1.6-kb NELFE transcript in all tissues examined.
Yamaguchi et al. (1999) described the identification and purification from HeLa nuclear extracts of a protein factor required for DRB (a nucleoside analog)-sensitive transcription. This factor, which they designated NELF, cooperates with DSIF and strongly represses pol II elongation. This repression is reversed by positive transcription elongation factor B (PTEFB)-dependent phosphorylation of the pol II C-terminal domain. NELF is composed of 5 polypeptides, the smallest of which, NELFE, is identical to RD.
Narita et al. (2003) reconstituted an active NELF-like complex by overexpressing epitope-tagged NELFA, NELFB, NELFD, and NELFE in insect cells. They found that the leucine zipper of NELFE interacted directly with NELFB and that NELFD interacted directly with NELFA and NELFB, consistent with a model in which NELFB and NELFD (or NELFC) bring NELFA and NELFE together via 3 protein-protein interactions. All 4 NELF subunits were required for NELF function.
Narita et al. (2007) showed that NELF interacted with the nuclear cap-binding complex (CBC), which plays roles in several mRNA processing steps. The interaction was mediated by NELFE and the CBC subunit CBP80 (NCBP1; 600469), and amino acids 244 to 380 of NELFE were required for the interaction. Small interfering RNA-mediated knockdown of NELFE or CBP80 in HeLa cells reduced the protein levels of other NELF and CBC subunits, respectively, suggesting that free NELF and CBC subunits are unstable in the absence of the functional holocomplexes. Knockdown of NELFE or CBP80 also resulted in elevated levels of polyadenylated histone mRNAs.
PARPs, such as PARP1 (173870), covalently transfer ADP-ribose from NAD+ onto substrate proteins. Using human cell lines, Gibson et al. (2016) found that PARP1 interacted with and ADP ribosylated NELFE. NELFA was also ADP ribosylated. ADP ribosylation of NELFE ablated the ability of NELF to bind RNA and released Pol II from NELF-dependent pausing. Depletion or inhibition of PARP1 in human cell lines, or mutation of the ADP-ribosylation sites on NELFE, promoted Pol II pausing. ADP-ribosylation of NELFE was dependent on prior phosphorylation of NELFE by PTEFB. Gibson et al. (2016) concluded that PARP1-dependent ADP ribosylation of phosphorylated NELFE is necessary for efficient release of Pol II into productive elongation.
Speiser and White (1989) determined that the RD gene contains 10 exons spread over approximately 6 kb of DNA.
Levi-Strauss et al. (1988) mapped the RD gene between the C4 (120810) and BF (138470) genes of the H-2 and HLA complexes of mouse and man, respectively (i.e., chromosome 17 and chromosome 6p21.3 for mouse and man, respectively).
Gibson, B. A., Zhang, Y., Jiang, H., Hussey, K. M., Shrimp, J. H., Lin, H., Schwede, F., Yu, Y., Kraus, W. L. Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science 353: 45-50, 2016. [PubMed: 27256882] [Full Text: https://doi.org/10.1126/science.aaf7865]
Levi-Strauss, M., Carroll, M. C., Steinmetz, M., Meo, T. A previously undetected MHC gene with an unusual periodic structure. Science 240: 201-204, 1988. [PubMed: 3353717] [Full Text: https://doi.org/10.1126/science.3353717]
Narita, T., Yamaguchi, Y., Yano, K., Sugimoto, S., Chanarat, S., Wada, T., Kim, D., Hasegawa, J., Omori, M., Inukai, N., Endoh, M., Yamada, T., Handa, H. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Molec. Cell. Biol. 23: 1863-1873, 2003. [PubMed: 12612062] [Full Text: https://doi.org/10.1128/MCB.23.6.1863-1873.2003]
Narita, T., Yung, T. M. C., Yamamoto, J., Tsuboi, Y., Tanabe, H., Tanaka, K., Yamaguchi, Y., Handa, H. NELF interacts with CBC and participates in 3-prime end processing of replication-dependent histone mRNAs. Molec. Cell 26: 349-365, 2007. [PubMed: 17499042] [Full Text: https://doi.org/10.1016/j.molcel.2007.04.011]
Speiser, P. W., White, P. C. Structure of the human RD gene: a highly conserved gene in the class III region of the major histocompatibility complex. DNA 8: 745-751, 1989. [PubMed: 2612324] [Full Text: https://doi.org/10.1089/dna.1989.8.745]
Surowy, C. S., Gosink, J. J., Spritz, R. A. cDNA cloning of the human 'RD' protein, a possible novel RNA-binding protein. (Abstract) Am. J. Hum. Genet. 43: A203 only, 1988.
Yamaguchi, Y., Takagi, T., Wada, T., Yano, K., Furuya, A., Sugimoto, S., Hasegawa, J., Handa, H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97: 41-51, 1999. [PubMed: 10199401] [Full Text: https://doi.org/10.1016/s0092-8674(00)80713-8]