Histone modification cross-talk: analytical tools and molecular mechanisms

Abstract

Chromatin function emerges from combinatorial patterns of histone post-translational modifications (PTMs) that are read, written, and erased by dedicated enzymes. Over the past 30years, increasing evidence suggests that specific histone PTMs or combinations of PTMs influence one another, constituting epigenetic cross-talk that shapes chromatin structure, protein-protein interactions, and catalytic efficiency of nucleosome-targeting enzymes. Here, we summarize mechanistic and methodological advances that enable rigorous interrogation of histone PTM interplay. We highlight selected nucleosome engineering strategies that build precisely modified substrates to test in vitro, proteomic pipelines that preserve combinatorial information, and omics technology that can globally profile integrated chromatin regulatory events in cells and tissues. Furthermore, we survey multivalent reader modules and engineered biosensors that report combinatorial marks in nucleosomes and living cells. Representative case studies illustrate how defined PTMs modulate catalytic parameters of writer and eraser complexes, including lysine methyltransferases, demethylases, acetyltransferases, and deacetylases, focusing on cross-talk with histone H3 N-terminal tail marks. These include the role of H3K9me2/3 and K14ac in directing propagation of H3K9me3, the role of H3K4me1/2 and K14ac in slowing H3K4 demethylation, the role of H3K4me2/3 in directing H3K9 acetylation, and the role of H3K36 methylation in directing deacetylation of H3 and H4. The substrates for these case studies include both mononucleosomes and nucleosome arrays. These examples illustrate the principle of epigenetic cross-talk, namely, that specific combinatorial PTMs can affect enzymes and alter local biochemistry.