Genetic and genomic techniques have proven incredibly powerful for identifying and studying molecular players implicated in the epigenetic regulation of DNA-templated processes such as transcription. However, achieving a mechanistic understanding of how these molecules interact with chromatin to elicit a functional output is non-trivial, owing to the tremendous complexity of the biochemical networks involved. Advances in protein engineering have enabled the reconstitution of ‘designer’ chromatin containing customized post-translational modification patterns, which, when used in conjunction with sophisticated biochemical and biophysical methods, allow many mechanistic questions to be addressed. In this Review, we discuss how such tools complement established ‘omics’ techniques to answer fundamental questions on chromatin regulation, focusing on chromatin mark establishment and protein–chromatin interactions.
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Some of the work discussed in this Review was conducted in the laboratory of T.W.M. and financially supported by the National Institutes of Health (NIH, R01 GM086868, R01 CA240768 and P01 CA196539) and Princeton Catalysis Initiative. N.H. is a Robert Black Fellow of the Damon Runyon Cancer Research Foundation, DRG-2425-21. S.K. is supported by the Human Frontier Science Program fellowship, LT000595/2020. We also thank members of the Muir lab past and present for helpful discussions in the preparation of this Review.
The authors declare no competing interests.
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Nature Reviews Genetics thanks Rodrigo Villaseñor, who co-reviewed with Namisha Rakesh, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
This Review is dedicated to the memory of C. David Allis.
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- Constitutive heterochromatin
Genomic regions containing a high density of repetitive DNA elements, found for example in centromeres and pericentromeric domains, which are packed in a stably inactive form.
- Designer chromatin
A reconstituted chromatin template comprising one or more chemically customized histone(s) containing site-specific post-translational modifications and/or a biochemical probe such as a photocrosslinker.
Heritable gene regulatory information that is not linked to changes in DNA sequence.
An enzyme that removes modifications from histones or DNA.
- Facultative heterochromatin
Genomic regions containing genes that are silenced in a cell type-specific or developmentally regulated manner. Various signals can reverse facultative heterochromatin repression to allow transcription.
- Histone PTM crosstalk
The ability of a preexisting post-translational modification (PTM) to impact the installation, removal or readout of another PTM. Crosstalk can occur between PTMs on the same histone (cis) or different histones (trans).
Here, it refers to the constellation of cellular factors that are recruited to a particular protein. Chromatin interactomes can change as a function of epigenetic modifications.
- Proximity labelling
A chemo-proteomic approach that allows the interactome around a protein of interest to be identified by ‘painting’ it with locally-activated chemical probes bearing an affinity handle such as biotin.
A protein that binds specifically to post-translationally-modified histones, thereby mediating the post-translational modification’s biological outcome.
An enzyme that adds modifications to histones or DNA.
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Hananya, N., Koren, S. & Muir, T.W. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet (2023). https://doi.org/10.1038/s41576-023-00664-z