Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

摘要

Background: In mammals, Ch IP-seq studies of RNA polymerase II (Pol II) occupancy have been performed to reveal how recruitment, initiation and pausing of Pol II may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of Pol II through sequential promoter states. Results: Here, we analyze Pol II binding profiles from high-coverage Ch IP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of Pol II near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial Pol II signal, gene by gene, we show that the first Pol II peak allows for refined positioning of transcription start sites, which is corroborated by m RNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as Cp G content and TATA boxes, as well as the histone mark H3K4me3. Conclusions: We thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of Pol II accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.