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

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 perform genomic analyses of features associated with active promoter chromatin in mouse embryonic stem cells (ESCs) and find evidence of subtle yet widespread promoter dysregulation in the absence of H3.3. Loss of H3.3 results in reduced chromatin accessibility and transcription factor (TF) binding at promoters of expressed genes in ESCs. Likewise, enrichment of the transcriptional coactivator p300 and downstream histone H3 acetylation at lysine 27 (H3K27ac) is reduced at promoters in the absence of H3.3, along with reduced enrichment of the acetyl lysine reader BRD4. 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 TF 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, transcription factor binding, and histone post-translational modification at active promoters. While H3.3 is not required for maintaining transcription in ESCs, it does promote de novo transcription factor binding which may contribute to the dysregulation of cellular differentiation in the absence of H3.3.

The role of chromatin state in intron retention: a case study in leveraging large scale deep learning models

“…This redundancy between histone marks and TF binding has also been observed in the context of prediction of gene expression [8]. This is not surprising, since histone marks contribute to TF binding [26,3], and vice versa -TFs help recruit histone modifiers [3]. Finally, an important advantage of the simple logistic regression approach over the finetuned Sei is that it is amenable to easy interpretation by looking at the weights assigned to the different targets as discussed next.…”

Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm

“…To determine whether the observed occupancy of CTCF sites is specific to the posterior trunk mesoderm, we performed footprinting analysis of publicly available ATAC-seq data and compared them with our data. We found that CTCF occupancy in mouse embryonic stem cells ( Metzis et al, 2018 ; Tafessu et al, 2023 ) and mouse embryonic fibroblasts ( Wang et al, 2019 ) exhibited significantly different CTCF occupancy patterns when compared with posterior trunk mesoderm ( Fig. S7 ).…”

Involvement of the H3.3 Histone Variant in the Epigenetic Regulation of Gene Expression in the Nervous System, in Both Physiological and Pathological Conditions

“…However, the precise mechanisms underlying how H3.3 causes chromatin opening are not completely clear. For example, using a genomic analysis on mouse embryonic stem cells in which H3.3 knockout had been induced, it was found that there is a general deregulation of promoter activity at the level of expressed genes associated with a reduction in transcription factor binding and a consequent reduction in RNA polymerase II at the transcription start sites [57]. Now, if we accept the principle that nuclear chromatin organization confers to each cell a specific phenotype because it represents the epigenetic memory of the history of that cell [99], then we have to admit that it will be even more so, and lifelong, for cells that are responsible for the macroscopic ability to learn and remember, namely neurons and probably also some glial cells such as astrocytes [100].…”