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The negative elongation factor NELF is a key component of an early elongation checkpoint generally located within 100 bp of the transcription start site of protein-coding genes. Negotiation of this checkpoint and conversion to productive elongation require phosphorylation of the carboxy-terminal domain of RNA polymerase II (pol II), NELF, and DRB sensitivity-inducing factor (DSIF) by positive transcription elongation factor b (P-TEFb). P-TEFb is dispensable for transcription of the noncoding U2 snRNA genes, suggesting that a NELF-dependent checkpoint is absent. However, we find that NELF at the end of the 800-bp U2 gene transcription unit and RNA interference-mediated knockdown of NELF causes a termination defect. NELF is also associated 800 bp downstream of the transcription start site of the beta-actin gene, where a "late" P-TEFb-dependent checkpoint occurs. Interestingly, both genes have an extended nucleosome-depleted region up to the NELF-dependent control point. In both cases, transcription through this region is P-TEFb independent, implicating chromatin in the formation of the terminator/checkpoint. Furthermore, CTCF colocalizes with NELF on the U2 and beta-actin genes, raising the possibility that it helps the positioning and/or function of the NELF-dependent control point on these genes.

Original publication




Journal article


Mol Cell Biol

Publication Date





4002 - 4013


Actins, Binding Sites, CCCTC-Binding Factor, Chromatin, DNA Polymerase II, DNA-Binding Proteins, HeLa Cells, High Mobility Group Proteins, Humans, Models, Biological, Nuclear Proteins, Nucleosomes, Phosphorylation, Positive Transcriptional Elongation Factor B, Promoter Regions, Genetic, Protein Structure, Tertiary, RNA Interference, RNA, Small Interfering, RNA, Small Nuclear, Recombinant Proteins, Repressor Proteins, Transcription Factors, Transcription, Genetic, Transcriptional Elongation Factors