Nucleosome conformation dictates the histone code

Abstract

Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized 'codes' that are read by specialized regions (reader domains) in chromatin associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP : histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher order factors. Here we show that the [BPTF PHD finger and bromodomain : histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the 'histone code' concept and interrogate it at the nucleosome level.

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

“…( 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 ].…”

“…To truly appreciate combinatorial chromatin interactions, it is essential to understand how various nucleosome features may be involved. A recent study re-evaluated the PTM preference of BPTF PHD–BD on libraries of fully defined peptides and nucleosomes in parallel [ 59 ] — an unbiased approach versus the more common of using positive peptide data to select nucleosomes for further study [ 211 ]. Results with peptides replicated the literature, with PHD–BD binding H3K4me3 and poly-acetylated H4 (H4Kac) or H3 (H3Kac), though no indication of co-operative engagement to the H3K4me3Kac combinatorial ( Figure 4B ).…”

“…Results with peptides replicated the literature, with PHD–BD binding H3K4me3 and poly-acetylated H4 (H4Kac) or H3 (H3Kac), though no indication of co-operative engagement to the H3K4me3Kac combinatorial ( Figure 4B ). However, on nucleosomes, PHD–BD lost engagement with H4Kac and showed >20-fold increased binding to H3K4me3Kac over either PTM class alone ( Figure 4B ) [ 59 ]. This synergy indicates the PHD–BD tandem was more capable than predicted from either individual reader.…”

“…Why did the BPTF tandem reader show reduced affinity on nucleosomes vs. histone peptides, even losing the ability to bind H4Kac? NMR suggests this is largely due to the default histone tail associations with DNA, which sets up a competitive landscape for reader engagement [ 59 ]. Acetylation weakens histone H3 tail contacts with DNA, which enhances BPTF PHD interactions with cis H3K4me3 [ 57 ].…”