No Epigenetic Modification is an Island: How Reader Proteins Functionally Interpret Complex Chromatin States

Like no man is an island and instead relies on those surrounding them, single epigenetic modifications generally do not function in solitary. Now, an absorbing new study from a synergistic epigenomics squad reports how epigenetic reader proteins functionally interpret chromatin states made up of complex combinations of disparate epigenetic modifications.

A highly collaborative team guided by Till Bartke (Helmholtz Zentrum München) knew of reader proteins that recognized individual modifications; however, the functional interpretation of complex chromatin states remained somewhat a mystery. To understand how chromatin readers decode said states, this combinatorial crew used multidimensional mass spectrometry-based chromatin profiling to examine the interaction of ~2,000 nucleosome-interacting proteins with ~80 semisynthetic dinucleosomes representing promoter/enhancer-associated permissive and repressive chromatin states.

Let’s hear more on the functional interpretation of chromatin states from Lukauskas, Tvardovskiy, Nguyen, and Colleagues:

• Chromatin profiling reveals characteristic nucleosome-binding behaviors, which you can explore through an interactive online visualization resource – Modification Atlas of Regulation by Chromatin States (MARCS)
• Responses by chromatin readers to repressive/activating states uncover two principal modes of interaction
  • Simple responses to single modifications (MECP2 recruitment/KDM2B exclusion by DNA methylation) and complex binding patterns indicating binding to multiple modifications/synergistic responses (e.g., ORC recruitment to H3K9, H3K27 or H4K20 methylation, further stimulated by DNA methylation)
  • Broad/unbiased chromatin profiling also identifies novel interactions with modified nucleosomes (e.g., INO80 and PRC1 enrichment on nucleosomes with active modification signatures)
• The resolution of chromatin reader responses to 15 modifications from 82 pairs of nucleosomes quantitatively describes chromatin binding by several hundred proteins and breaks down complex binding profiles into critical features that positively/negatively regulate associations with modified nucleosomes
  • Euchromatic features recruit/exclude many more proteins than heterochromatic features
  • Protein regulation by more than one feature indicates independent responses to multiple modifications or the recognition of composite modification signatures
  • Clustering of protein binding behaviors revealed a grouping of 40 major binding responses defined by multisubunit protein complexes
• Reconstructing protein networks co-regulated by similar chromatin states predicts protein-protein interactions, with chromatin regulatory complexes forming clusters of separate complexes/high-confidence binary interactions
  • Co-regulated protein network responses to chromatin features reveal the differential binding of factors to H3 and H4 acetylation, suggesting an orchestrated regulation of active chromatin states by differential acetylation

Ultimately, this exceptional study reveals that no epigenetic modification is an island! “Epigenetic modifications usually act in cooperation with so-called epigenetic reader proteins that recognize them and promote downstream effects,” explains Dr. Andrey Tvardovskiy, post-doctoral researcher and one of the study’s first authors. “Uncovering how epigenetic readers interpret such complex modification signatures is therefore key to understanding how our genome functions and how its misregulation can lead to human diseases.”

For more on how “no man is an island,” the functional interpretation of chromatin states, and all the future applications, see Nature, March 2024.