Interdependence between histone marks and steps in Pol II transcription

Abstract

The role of histone modifications in transcription remains incompletely understood. Here we used experimental perturbations combined with sensitive machine learning tools that infer the distribution of histone marks using maps of nascent transcription. Transcription predicted the variation in active histone marks and complex chromatin states, like bivalent promoters, down to single-nucleosome resolution and at an accuracy that rivaled the correspondence between independent ChIP-seq experiments. Blocking transcription rapidly removed two punctate marks, H3K4me3 and H3K27ac, from chromatin indicating that transcription is required for active histone modifications. Transcription was also required for maintenance of H3K27me3 consistent with a role for RNA in recruiting PRC2. A subset of DNase-I hypersensitive sites were refractory to prediction, precluding models where transcription initiates pervasively at any open chromatin. Our results, in combination with past literature, support a model in which active histone modifications serve a supportive, rather than a regulatory, role in transcription.

RNA polymerase II and PARP1 shape enhancer-promoter contacts

“…We first analyzed seven CRISPRi-defined enhancers that regulate MYC expression in K562 cells ( 28 ), all of which fall within the same topologically associated domain (TAD) as the MYC protein-coding gene. Each of the seven active MYC enhancers was located near a transcription initiation region (TIR), representing the transcription start site of an enhancer RNA (eRNA), identified from dREG ( 30, 31 ) analysis of K562 PRO-seq data ( 32 ) ( Fig. 1A ).…”

“…We therefore examined the enrichment of functional contacts as a function of distance from the TSS. Active enhancers and promoters consist of a nucleosome-free core region flanked by bidirectional transcription initiation and well-positioned +1 and +2 nucleosomes downstream of the most-used TSS (33)(34)(35) that are readily observed in Micro-C data after aligning on coPRO TSSs (32,36) (Fig. S2).…”

RNA polymerase II dynamics shape enhancer–promoter interactions

“…We rst analyzed seven CRISPRi-de ned enhancers that regulate MYC expression in K562 cells 28 , all of which fall within the same topologically associated domain (TAD) as the MYC protein-coding gene. Each of the seven active MYC enhancers was located near a transcription initiation region (TIR), representing the transcription start site of an enhancer RNA (eRNA), identi ed from dREG 30,31 analysis of K562 PROseq data 32 (Fig. 1A).…”

“…We therefore examined the enrichment of functional contacts as a function of distance from the TSS. Active enhancers and promoters consist of a nucleosome-free core region anked by bidirectional transcription initiation and well-positioned + 1 and + 2 nucleosomes downstream of the most-used TSS [33][34][35] that are readily observed in Micro-C data after aligning on coPRO TSSs 32,36 (Fig. S2).…”

RNA polymerase II and PARP1 shape enhancer-promoter contacts

“…We rst analyzed seven CRISPRi-de ned enhancers that regulate MYC expression in K562 cells 28 , all of which fall within the same topologically associated domain (TAD) as the MYC protein-coding gene. Each of the seven active MYC enhancers was located near a transcription initiation region (TIR), representing the transcription start site of an enhancer RNA (eRNA), identi ed from dREG 30,31 analysis of K562 PROseq data 32 (Fig. 1A).…”