TRIM 28 regulates RNA polymerase

The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. et al. 2014. " TRIM28 regulates RNA polymerase II promoter proximal pausing and pause release. " Nature structural & molecular biology 21 (10): 876-883. Summary Promoter proximal pausing of RNA polymerase II (Pol II) is a major checkpoint in transcription. An unbiased search for novel human proteins that could regulate paused Pol II at the HSPA1B gene identified TRIM28. In vitro analyses indicated HSF1-dependent attenuation of Pol II pausing upon TRIM28 depletion, whereas in vivo data revealed de novo expression of HSPA1B and other known genes regulated by paused Pol II upon TRIM28 knockdown. These results were supported by genome-wide ChIP-sequencing analyses of Pol II occupancy that revealed a global role for Accession Code ChIP-seq genomic data described in this study have been deposited in the Gene Expression Omnibus under accession number GSE48253. Author Contributions: XZ and GH generated WT and TRIM28 KD mES cell extracts for ChIP-seq and ChIP-qPCR. SM and SL processed ChIP-seq. AB, GH, and DF performed Bioinformatics. STD and CE carried out MS. GB constructed TRIM28 plasmids. HB, DJT, and SKC designed the experiments and wrote the manuscript. TRIM28 in regulating Pol II pausing and pause release. Furthermore, in vivo and in vitro mechanistic studies suggest that transcription-coupled phosphorylation regulates Pol II pause release by TRIM28. Collectively, our findings identify TRIM28 as a novel factor that modulates Pol II pausing and transcriptional elongation at a large number of mammalian genes. Promoter proximal pausing of RNA polymerase II (Pol II) represents a major checkpoint in transcription. Typically, Pol II enzymes pause at around +30–100 relative to the transcriptional start site (TSS) until activating cellular signals induce elongation 1. Although promoter proximal pausing was discovered over two decades ago, it was initially thought to occur at only a limited set of genes 2. Recently however, genome-wide analyses such as Chromatin Immuno-Precipitation followed by sequencing (ChIP-seq) and Global Run-On Sequencing (GRO-seq) have shown that promoter-proximal pausing is widespread 1,3–7. For instance, approximately 30% of coding genes and over 70% of developmental or inducible genes harbor Pol II paused at promoter-proximal sites 8,9. Thus, promoter-proximal pausing is considered a major cellular mechanism to regulate gene expression. Although the mechanisms of Pol II pausing and pause release are incompletely understood, several transcription factors are known to regulate these processes. DSIF and NELF …