H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements

Abstract

Background: The histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are highly accessible, creating an environment that is permissive to transcription factor binding and the recruitment of transcriptional coactivators that establish a unique chromatin post-translational landscape. How H3.3 contributes to the establishment and function of chromatin states at these regions is poorly understood. Results: We performed genomic analyses of features associated with active promoter chromatin in mouse embryonic stem cells (ESCs) and found evidence of subtle yet widespread promoter dysregulation in the absence of H3.3. Loss of H3.3 deposition at promoters reduces chromatin accessibility and transcription factor (TF) footprinting for nearly all TFs expressed in ESCs. H3.3 deletion leads to reduced promoter enrichment of the transcriptional coactivator and histone acetyltransferase, p300. Subsequently, histone H3 acetylation at lysine 27 (H3K27ac) is reduced at promoters in the absence of H3.3, along with reduced enrichment of the bromodomain-containing protein BRD4, an acetyl lysine reader. Despite the observed chromatin dysregulation, H3.3 KO ESCs maintain transcription from ESC-specific genes. However, upon undirected differentiation, H3.3 KO cells retain footprinting of ESC-specific TFs motifs and fail to generate footprints of lineage-specific TF motifs, in line with their diminished capacity to differentiate. Conclusions: H3.3 facilitates DNA accessibility, TF binding, and histone post-translational modification at active promoters. While H3.3 is not required for maintaining transcription in ESCs, it is required for TF binding at new promoters during differentiation.

Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells

“…Rather than maintaining an already established transcriptional program, H3.3 seems to promote gene activation de novo 90,[94][95][96] . This is also supported by recent data in which HIRA-mediated depletion of H3.3 was associated with small, yet significant, loss of accessibility and TF binding at gene promoters and altered cellular differentiation 97 . Here, depleting HIRA in mESCs resulted in a significant reduction in histone exchange at open chromatin, suggesting that H3.3 deposition promotes nucleosome dynamics at these sites.…”

H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells

“…Data availability Datasets are deposited in the NCBI Gene Expression Omnibus using the following accession numbers: SuperSeries GSE186687, ATAC-seq GSE186684, ChIP-seq GSE186685, GRO-seq GSE186686, and CUT&Tag GSE213039 [ 89 ]. Other datasets used for this study are available under GSE114551 [ 25 , 90 ] and GSE151058 [ 46 , 91 ].…”