A unique H2B acetylation signature marks active enhancers and predicts their target genes

Abstract

Chromatin features are widely used for genome-scale mapping of enhancers. However, discriminating active enhancers from other cis-regulatory elements, predicting enhancer strength, and identifying their target genes remains challenging. Here we establish histone H2B N-terminus multisite lysine acetylation (H2BNTac) as a genuine signature of active enhancers. H2BNTac prominently marks candidate active enhancers and their target promoters and discriminates them from ubiquitously active promoters. Two mechanisms afford the distinct H2BNTac specificity. (1) Unlike H3K27ac, H2BNTac is specifically catalyzed by CBP/p300. (2) H2A-H2B, but not H3-H4, are rapidly exchanged through transcription-induced nucleosome remodeling. H2BNTac-positive candidate enhancers show a high validation rate in orthogonal enhancer activity assays, and a vast majority of endogenously active enhancers are marked by H2BNTac and H3K27ac. Notably, H2BNTac intensity predicts enhancer strength and outperforms the current state-of-the-art models in predicting enhancer target genes. These findings have broad implications for generating fine-grained enhancer maps and modeling enhancer-dependent gene regulation.

Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation

“…Consistent with our data, recent work mutating H3 and/or H3.3 Lysine 27 sites to Arginine, which cannot be acetylated did not impact either naive gene expression or the activation of the formative program in differentiating ESCs [14,15]. However, these findings are interpreted as a lack of a requirement for H3K27ac rather than an inability to recruit enhancer CBP/P300 at large where we also expect a loss in other active enhancer histone acetylations deposited by CBP/P300 such as H2B acetylation [42]. Either way, it is unclear whether many of the sites dependent on MLL3/4 for active histone marks are dispensable for gene expression changes and or these sites are functional enhancers without an active histone signature.…”

Epigenetic mechanisms to propagate histone acetylation by p300/CBP

“…Although H3K27ac, a residue acetylated by p300/CBP, has been used as a marker for active promoters and enhancers 17 , it is absent in many p300-enriched chromatin regions 18 and is dispensable for enhancer activity of gene transcription in mouse embryonic stem cells 19 . In contrast, possibly through transcription-coupled histone exchange, H2BNTac better correlates with enhancer activity than any other known chromatin marks, with RNA transcription found in 79% of all H2BNTac-positive regions 16 . Importantly, the acetyltransferase activity of p300 responsible for H2BNTac 15 is a key driver of rapid enhancer activation and is essential for promoting the recruitment of RNA polymerase II (RNAPII) at virtually all enhancers and enhancer-regulated genes 20 .…”

“…Indeed, p300 acetylates NT of H2A.Z, an evolutionarily conserved variant of H2A, through the bromodomain-mediated H4NTac 'reader' activity 14 . Interestingly, H2BNT is acetylated only by p300/CBP 15 , which is considered a genuine signature of active enhancers and their target promoters 16 .…”

Factors and Mechanisms That Influence Chromatin-Mediated Enhancer–Promoter Interactions and Transcriptional Regulation

“…Histone modification is widely used as a means to classify enhancers according to their activity: H3K4me1 and the binding of trithorax-related mixed lineage leukemia (MLL) complex define primed or active enhancers; H3K27me3 is a key marker of poised or inactive enhancers; histone H3 lysine 27 acetylation (H3K27ac) is a hallmark of transcriptionally active enhancers ( Figure 1 ) [ 11 , 12 , 13 , 14 ]. Recent trends highlight that rather than defining active enhancers with H3K27ac, different histone acetylation marks, such as simultaneous acetylation of histone H4 at both K5 and K8 (H4K5acK8ac) [ 15 ], Das et al, [submitted], histone H2B N-terminus multisite lysine (e.g., K5, K12, K16, and K20) acetylation (H2BNTac [ 16 ]), H3K122ac [ 17 ], and H4K16ac [ 18 ], to define active enhancers are emerging. A large number of histone modifications have been implicated in gene transcription, where H3K4me3 has been associated with gene promoter regions [ 19 ].…”

“…Importantly, local chromatin features, including marks indicating active (H3K27ac; [ 98 ]) or repressed (HP1 and H3K27me3; [ 97 ] chromatin, the presence of linker histone H1 proteins, and the associated TFs [ 103 ] cooperate in forming or dissolving phase-separated condensates ( Figure 2 ). In addition, newly identified marks of active enhancers, such as histone H4 hyperacetylation (H4K5acK8ac; Das et al, submitted) and H2BNTac [ 16 ], may contribute to the formation of phase-separated condensates. As directed by local chromatin features (e.g., in SEs), such phase-separated condensates could mediate systematic loading of the transcriptional machinery to active gene promoters [ 102 ], thus facilitating the E–P interactions.…”