Beyond the tail: the consequence of context in histone post-translational modification and chromatin research

Abstract

The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.

Keywords: chromatin; histone code; histone peptides; histone post-translational modifications; histones; nucleosome.

Figure 1.. Our increasing understanding of chromatin biology, nucleosome structure, and histone PTM function was driven by continued technological innovation and improvement.

(A) Pre-2000. (B) 2000–2020. Key discoveries are denoted by year and specific innovations within each time period noted. Key: ChIP, chromatin immunoprecipitation; KAT, lysine acetyltransferase; KDAC, lysine deacetylase; NMR, nuclear magnetic resonance, cryo-EM, cryogenic electron microscopy; KDM, lysine demethylase; KMT, lysine methyltransferase. Figure created with BioRender.

Figure 2.. The histone tails make extensive (and regulatable) contacts with the nucleosome core particle.

(A) Original crystal structures of the nucleosome [40] could not visualize N-terminal tails, leading many to assume they protrude from the core into solution [55,56]. (B) However, NMR shows that unmodified, positively-charged histone tails collapse onto the nucleosome surface, and make extensive contacts with negatively charged DNA and the H2A/H2B acidic patch [57,58]. (C) Acetylation neutralizes tail positive charge and disrupts these interactions, highlighting the role of nucleosome electrostatics in chromatin interactions [57,59]. Other PTMs that modulate charge include the larger family of lysine acylations [60], serine and threonine phosphorylation [61], or arginine deimination/citrullination [62]. Figure created with BioRender.

Figure 3.. Potential mechanisms and functions of combinatorial histone PTMs as outlined in the original ‘histone code’ hypothesis [61].

(A) Key elements of the language. (B,C) Examples of readout include where sequential histone PTMs facilitate gene activation (B), or combinatorial histone PTMs regulate gene activation (C). Figure created with BioRender.

Figure 4.. Studies of MLL1-C lysine methyltransferase complex and the BPTF PHD-BD tandem reader illustrate the importance of nucleosome context for chromatin research [59,192].

(A) A coherent mechanism links H3 tail acetylation, H3K4 methylation, and BPTF binding. Acetylation reduces H3 tail affinity for nucleosomal DNA, allowing MLL1-C to effectively catalyze H3K4me3 in cis. The BPTF PHD-BD tandem reader requires both H3K4me3 and H3K14ac/H3K18ac in cis for synergistic binding. (B) Experimental results demonstrate key differences in BPTF binding between peptide and nucleosome substrates. Interestingly, though the Kac and Kme cross-talk occurs on the same nucleosomal H3 tail (i.e. cis vs. trans), this interplay is not detected on peptides. Figure created with BioRender.

Figure 5.. Allosteric activation of DOT1L methyltransferase requires multivalent engagement with a H2BK120ub1 nucleosome substrate [275–278].

DOT1L recruitment to a H2BK120ub1 nucleosome is stabilized through interactions with the H2A/H2B acidic patch. To convert from ‘resting’ to ‘active’ state, DOT1L binds the H4 tail (brown), which drives conformational changes that place H3K79 within the enzyme active site. Adapted from [277]. Figure created with BioRender.