Science has moved on since William Shakespeare put quill to parchment around 1600 to write the Tragedy of Hamlet, Prince of Denmark, but his legacy has survived to influence a new manuscript that describes the quest to discover histone modifications that better distinguish active enhancers. “H2B, or not H2B, that is the question!”
Enhancer elements throughout the genome activate signal-induced and developmentally regulated genes, with candidates generally identified by detecting histone modifications such as H3K4me1 and H3K27ac; however, multiple obstacles impede a deeper understanding of enhancer-dependent gene regulation. Epigenetic playwrights directed by Chunaram Choudhary (University of Copenhagen, Denmark) sought to overcome these stumbling blocks to identify active enhancers from other cis-regulatory elements, predict enhancer strength, and discover target genes by focusing on H2B N-terminus multisite lysine acetylation (H2BNTac) as an alternative to the oft used H3K27ac histone modification.
Let’s hear about this Shakespearean study from the inky-fingered, candle-wax-spattered team of Narita and Colleagues:
- ChIP-seq analysis using mouse embryonic stem cells and human cancer cells reveals H2BNTac and H3K27ac occupancy and locus-specific regulation
- Most H3K27ac and H2BNTac peaks occur at highly accessible regions (as measured by ATAC-seq)
- Strongly H2BNTac-modified regions generally contain H3K27ac; however, many abundantly H3K27ac-modified regions lack H2BNTac
- H2BNTac distinctively marks candidate active enhancers and so distinguishes them from other regulatory regions
- Specific catalysis of H2BNTac by CBP/p300 (unlike H3K27ac) and the rapid exchange of H2A–H2B (but not H3–H4) through transcription-induced nucleosome remodeling appear to underlie the distinct specificity of H2BNTac
- H2BNTac-positive candidate enhancers display elevated validation rates in orthogonal enhancer activity assays (enhancer RNA transcription and massively parallel reporter assays)
- H2BNTac most accurately defines locus-specific CBP/p300 activity and enhancer strength
- H2BNTac also outperforms H3K27ac in predicting CBP/p300-regulated genes (when evaluated using the activity-by-contact model integrating ATAC–seq, Hi-C contact frequency, and H3K27ac or H2BNTac ChIP signal or H2BNTac intensity alone) and the degree of dependency on CBP/p300 activity
The discovery that H2BNTac can distinguish active enhancers is no tragedy; indeed, these findings should provide impetus to the development of fine-grained enhancer maps and the further exploration of CBP/p300-dependent gene regulation. Of note, the authors state that there’s room for improvement with CBP/p300 target gene prediction accuracy and a need to further investigate the biological relevance of H2BNTac.
To read or not to read should not be the question; see all the details on this new study at Nature Genetics, April 2023.