The histone variant H2A.Z is an important regulator of enhancer activity.

Mylène Brunelle,Nicolas Gévry,Mathieu Lupien,Alexei Nordell Markovits,Pierre-Étienne Jacques,Sébastien Rodrigue

doi:10.1093/nar/gkv825

Abstract

Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles in transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate by genome-wide approaches that H2A.Z is present at a subset of active enhancers bound by the estrogen receptor alpha (ERα). We also determine that H2A.Z does not influence the local nucleosome positioning around ERα enhancers using ChIP sequencing at nucleosomal resolution and unsupervised pattern discovery. We further highlight that H2A.Z-enriched enhancers are associated with chromatin accessibility, H3K122ac enrichment and hypomethylated DNA. Moreover, upon estrogen stimulation, the enhancers occupied by H2A.Z produce enhancer RNAs (eRNAs), and recruit RNA polymerase II as well as RAD21, a member of the cohesin complex involved in chromatin interactions between enhancers and promoters. Importantly, their recruitment and eRNAs production are abolished by H2A.Z depletion, thereby revealing a novel functional link between H2A.Z occupancy and enhancer activity. Taken together, our findings suggest that H2A.Z acts as an important player for enhancer functions by establishing and maintaining a chromatin environment required for RNA polymerase II recruitment, eRNAs transcription and enhancer-promoters interactions, all essential attributes of enhancer activity.

Highlights

Enhancers play a central role in achieving cell-type and cell-state-specific transcriptional programs, by integrating signals through the recruitment of specific transcription factors (TFs) and co-activator complexes in order to coordinate gene regulation of different subsets of target genes [1,2,3]
Considering that potential unannotated promoters could bias the interpretation of the role of H2A.Z at enhancers when the classification is only guided by gene annotations, and to clarify the relationship between H2A.Z and H3K4me3 in regard to enhancers, we analyzed both proximal and distal H2A.Z-enriched regions, as well as distal ER␣-BS [45]
We observed that regions co-enriched for H2A.Z and H3K4me3 mostly harbor promoter properties, regardless of whether these regions are proximal or distal to a known Transcription Start Site (TSS) (Supplementary Figure S2), indicating that distal regions are likely to be contaminated by unannotated promoters

Summary

Introduction

Enhancers play a central role in achieving cell-type and cell-state-specific transcriptional programs, by integrating signals (e.g., from developmental, differentiation or hormonal stimuli) through the recruitment of specific transcription factors (TFs) and co-activator complexes in order to coordinate gene regulation of different subsets of target genes [1,2,3]. Enhancers identification is crucial to understand physiological and pathological processes, such as the extensive deregulation of gene expression patterns observed in cancer [4]. It is achievable by exploiting the dichotomy of lysine 4 methylation (me) status of histone H3 (H3K4) between enhancers and promoters. The step to understand the role of this main regulator of gene expression is to elucidate the mechanisms responsible for enhancer functions at the chromatin level

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