Histone H3K27 acetylation is dispensable for enhancer activity in mouse embryonic stem cells

Abstract

H3K27ac is well recognized as a marker for active enhancers and a great indicator of enhancer activity. However, its functional impact on transcription has not been characterized. By substituting lysine 27 in histone variant H3.3 with arginine in mouse embryonic stem cells, we diminish the vast majority of H3K27ac at enhancers. However, the transcriptome is largely undisturbed in these mutant cells, likely because the other enhancer features remain largely unchanged, including chromatin accessibility, H3K4me1, and histone acetylation at other lysine residues. Our results clearly reveal that H3K27ac alone is not capable of functionally determining enhancer activity.

The TAZ2 domain of CBP/p300 directs acetylation towards H3K27 within chromatin

“…Finally, the dCas9-based targeting experiments presented here add to our understanding of the role of H3K27ac in transcriptional activation. Consistent with recent observations that H3K27ac is not uniquely important for maintaining gene expression (Zhang et al, 2020), we found that the presence of H3K27ac alone is not sufficient to generate high levels of transcription, but requires co-occurrence of at least H3K27ac and H3K9ac ( Figure 5). These observations support a model in which multiple histone acetylation marks, including H3K27ac, function in concert to maintain full and robust transcriptional activation of target genes, while enabling complex regulation and integration of multiple inputs via concerted action of multiple HATs, specific acetylation marks, their cognate readers and direct impact on chromatin structure ( Figure 6).…”

“…Histone acetylation marks at different residues commonly co-occur in combinatorial fashion, colocalizing at regulatory regions of actively transcribed genes (Birney et al, 2007;Heintzman et al, 2007;Wang et al, 2008). Indeed, acetylation of histone H3 lysine 9 (H3K9), H3K18, H3K27, and of several residues within the N-terminal tail of histone H4 have all been shown to correlate with active promoters and enhancers (Creyghton et al, 2010;Karmodiya et al, 2012;Rada-Iglesias et al, 2011;Wang et al, 2009;Wang et al, 2008;Zhang et al, 2020) Despite this extensive cooccurrence, specific functions have been demonstrated for individual acetylation marks, including H4K16ac in regulating interactions between neighbouring nucleosomes (Shogren-Knaak et al, 2006) and H3K9ac in facilitating recruitment of the basal transcription factor TFIID (Vermeulen et al, 2007). These observations suggest cooperative rather than redundant functions for specific acetylation marks, highlighting the importance of HAT substrate specificity for proper regulation of transcription.…”

Interdependence between histone marks and steps in Pol II transcription

“…The high correlation between histone modifications and transcription has important consequences for the way we understand the role of histone modifications. Despite decades of speculation about the regulatory role of many histone modifications, recent studies depleting histone modifications widely believed to be critical for transcription result in surprisingly limited effects on gene expression (75)(76)(77). Our incomplete knowledge about the role that histone modifications play in transcription results in part from a lack of information about precisely how strong the correspondence between histone modifications and transcription actually is.…”

Functional mapping of androgen receptor enhancer activity

“…These features all broadly correlate with active enhancers but they are not causative and are therefore extremely prone to false positives 14 . For example , global loss of enhancer mark H3K27ac has no functional impact on gene transcription, chromatin accessibility or histone modifications 15 . Therefore, episomal reporter assays, which quantify the enhancer induced transcription of a gene, still remain the cornerstone of enhancer validation 16 .…”