NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

• Published in: Molecular cell 2020-04, Vol.78 (2), p.261-274.e5
• Main Authors: Aoi, Yuki, Smith, Edwin R., Shah, Avani P., Rendleman, Emily J., Marshall, Stacy A., Woodfin, Ashley R., Chen, Fei X., Shiekhattar, Ramin, Shilatifard, Ali
• Format: Article
• Language: English
• Subjects: Animals; cap-binding complex; Heat-Shock Response - genetics; Humans; m7G cap; Mice; mRNA capping; NELF; Nucleosomes - genetics; Positive Transcriptional Elongation Factor B - genetics; PRO-cap; PRO-seq; Promoter Regions, Genetic; promoter-proximal pausing; RNA Polymerase II; RNA Polymerase II - genetics; super elongation complex; transcription elongation; Transcription Factors - genetics; Transcription, Genetic
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2020.02.014

RNA polymerase II (RNA Pol II) is generally paused at promoter-proximal regions in most metazoans, and based on in vitro studies, this function has been attributed to the negative elongation factor (NELF). Here, we show that upon rapid depletion of NELF, RNA Pol II fails to be released into gene bodies, stopping instead around the +1 nucleosomal dyad-associated region. The transition to the 2nd pause region is independent of positive transcription elongation factor P-TEFb. During the heat shock response, RNA Pol II is rapidly released from pausing at heat shock-induced genes, while most genes are paused and transcriptionally downregulated. Both of these aspects of the heat shock response remain intact upon NELF loss. We find that NELF depletion results in global loss of cap-binding complex from chromatin without global reduction of nascent transcript 5′ cap stability. Thus, our studies implicate NELF functioning in early elongation complexes distinct from RNA Pol II pause-release. [Display omitted] •Acute NELF depletion reveals 2-step pausing of RNA Pol II at promoters•The 1st-to-2nd pausing transition is independent of P-TEFb/SEC activity•The heat shock response remains intact in the absence of NELF•NELF recruits the cap-binding complex with modest effects on 5′ cap stability Metazoan RNA Pol II-transcribed genes exhibit post-initiation regulation called pausing. Aoi et al. find that loss of the protein complex thought to maintain pausing, NELF, does not result in global release of RNA Pol II but instead may regulate other promoter-proximal regulatory steps such as 5′ mRNA cap stability.