Abstract
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.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Millán-Zambrano, G., Burton, A., Bannister, A. J. & Schneider, R. Histone post-translational modifications — cause and consequence of genome function. Nat. Rev. Genet. 23, 563–580 (2022).
Zhao, S., Allis, C. D. & Wang, G. G. The language of chromatin modification in human cancers. Nat. Rev. Cancer 21, 413–430 (2021).
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007).
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Rotem, A. et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol. 33, 1165–1172 (2015).
Ziegenhain, C. et al. Comparative analysis of single-cell RNA sequencing methods. Mol. Cell 65, 631–643 (2017).
Lusser, A. & Kadonaga, J. T. Strategies for the reconstitution of chromatin. Nat. Methods 1, 19–26 (2004).
Müller, M. M. & Muir, T. W. Histones: at the crossroads of peptide and protein chemistry. Chem. Rev. 115, 2296–2349 (2015).
Cuvier, O. & Fierz, B. Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. Nat. Rev. Genet. 18, 457–472 (2017).
Fierz, B. & Poirier, M. G. Biophysics of chromatin dynamics. Annu. Rev. Biophys. 48, 321–345 (2019).
Mitchener, M. M. & Muir, T. W. Oncohistones: exposing the nuances and vulnerabilities of epigenetic regulation. Mol. Cell 82, 2925–2938 (2022).
Maksimovic, I. & David, Y. Non-enzymatic covalent modifications as a new chapter in the histone code. Trends Biochem. Sci. 46, 718–730 (2021).
Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).
Probst, A. V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 10, 192–206 (2009).
Krieger, D. E., Levine, R., Merrifield, R. B., Vidali, G. & Allfrey, V. G. Chemical studies of histone acetylation. Substrate specificity of a histone deacetylase from calf thymus nuclei. J. Biol. Chem. 249, 332–334 (1974).
Krieger, D. E., Vidali, G., Erickson, B. W., Allfrey, V. G. & Merrifield, R. B. The synthesis of diacetylated histone H4-(1–37) for studies on the mechanism of histone deacetylation. Bioorg. Chem. 8, 409–427 (1979).
Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).
Hansen, K. H. et al. A model for transmission of the H3K27me3 epigenetic mark. Nat. Cell Biol. 10, 1291–1300 (2008).
Margueron, R. et al. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461, 762–767 (2009).
Schmitges, F. W. et al. Histone methylation by PRC2 is inhibited by active chromatin marks. Mol. Cell 42, 330–341 (2011).
Musselman, C. A. & Kutateladze, T. G. Strategies for generating modified nucleosomes: applications within structural biology studies. ACS Chem. Biol. 14, 579–586 (2019).
Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022).
Sankar, A. et al. Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals. Nat. Genet. 54, 754–760 (2022).
Grewal, S. I. S. The molecular basis of heterochromatin assembly and epigenetic inheritance. Mol. Cell 83, 1767–1785 (2023).
Fitz-James, M. H. & Cavalli, G. Molecular mechanisms of transgenerational epigenetic inheritance. Nat. Rev. Genet. 23, 325–341 (2022).
Allshire, R. C. & Madhani, H. D. Ten principles of heterochromatin formation and function. Nat. Rev. Mol. Cell Biol. 19, 229–244 (2018).
Zhang, K., Mosch, K., Fischle, W. & Grewal, S. I. S. Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat. Struct. Mol. Biol. 15, 381–388 (2008).
Al-Sady, B., Madhani, H. D. & Narlikar, G. J. Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread. Mol. Cell 51, 80–91 (2013).
Müller, M. M., Fierz, B., Bittova, L., Liszczak, G. & Muir, T. W. A two-state activation mechanism controls the histone methyltransferase Suv39h1. Nat. Chem. Biol. 12, 188–193 (2016).
Poepsel, S., Kasinath, V. & Nogales, E. Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. Nat. Struct. Mol. Biol. 25, 154–162 (2018).
Ge, E. J., Jani, K. S., Diehl, K. L., Müller, M. M. & Muir, T. W. Nucleation and propagation of heterochromatin by the histone methyltransferase PRC2: geometric constraints and impact of the regulatory subunit JARID2. J. Am. Chem. Soc. 141, 15029–15039 (2019). Through biochemical assays utilizing a variety of heterotypic designer nucleosome arrays, this study uncovers the geometric constraints of H3K27me3 propagation and demonstrates how differentially modified JARID2 regulates PRC2 substrate preferences.
Sanulli, S. et al. Jarid2 methylation via the PRC2 complex regulates H3K27me3 deposition during cell differentiation. Mol. Cell 57, 769–783 (2015).
Oksuz, O. et al. Capturing the onset of PRC2-mediated repressive domain formation. Mol. Cell 70, 1149–1162 (2018).
Kasinath, V. et al. JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications. Science 371, eabc3393 (2021).
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).
Voigt, P., Tee, W.-W. & Reinberg, D. A double take on bivalent promoters. Genes Dev. 27, 1318–1338 (2013).
Zhang, T., Cooper, S. & Brockdorff, N. The interplay of histone modifications – writers that read. EMBO Rep. 16, 1467–1481 (2015).
Worden, E. J. & Wolberger, C. Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases. Curr. Opin. Struct. Biol. 59, 98–106 (2019).
Briggs, S. D. et al. Trans-histone regulatory pathway in chromatin. Nature 418, 498 (2002).
Ng, H. H., Xu, R.-M., Zhang, Y. & Struhl, K. Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J. Biol. Chem. 277, 34655–34657 (2002).
Zhu, B. et al. Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. Mol. Cell 20, 601–611 (2005).
McGinty, R. K., Kim, J., Chatterjee, C., Roeder, R. G. & Muir, T. W. Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature 453, 812–816 (2008).
Holt, M. T. et al. Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin. Proc. Natl Acad. Sci. USA 112, 10365–10370 (2015).
Zhou, L. et al. Evidence that ubiquitylated H2B corrals hDot1L on the nucleosomal surface to induce H3K79 methylation. Nat. Commun. 7, 10589 (2016).
Worden, E. J., Hoffmann, N. A., Hicks, C. W. & Wolberger, C. Mechanism of cross-talk between H2B ubiquitination and H3 methylation by Dot1L. Cell 176, 1490–1501 (2019). This study determines the structure of Dot1L bound to H2BK120-ubiquitinated nucleosomes in poised and active states, revealing a unique conformational plasticity in the H3 globular core that underlines the H2BK120ub–H3K79me crosstalk.
Anderson, C. J. et al. Structural basis for recognition of ubiquitylated nucleosome by Dot1L methyltransferase. Cell Rep. 26, 1681–1690 (2019).
Valencia-Sánchez, M. I. et al. Structural basis of Dot1L stimulation by histone H2B lysine 120 ubiquitination. Mol. Cell 74, 1010–1019 (2019).
Ai, H. et al. H2B Lys34 ubiquitination induces nucleosome distortion to stimulate Dot1L activity. Nat. Chem. Biol. 18, 972–980 (2022).
Wojcik, F. et al. Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. Nat. Commun. 9, 1394 (2018).
Parreno, V., Martinez, A.-M. & Cavalli, G. Mechanisms of Polycomb group protein function in cancer. Cell Res. 32, 231–253 (2022).
Cao, R. et al. Role of histone H3 lysine 27 methylation in polycomb-group silencing. Science 298, 1039–1043 (2002).
Kalb, R. et al. Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat. Struct. Mol. Biol. 21, 569–571 (2014). By combining an unbiased proteomic screen with in vitro biochemical experiments, this study shows that H2A119 ubiquitination is recognized by and stimulates the activity of JARID2-AEBP2-containing PRC2.
Blackledge, N. P. et al. PRC1 catalytic activity is central to polycomb system function. Mol. Cell 77, 857–874.e9 (2020).
Blackledge, N. P. et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 157, 1445–1459 (2014).
Audia, J. E. & Campbell, R. M. Histone modifications and cancer. Cold Spring Harb. Perspect. Biol. 8, a019521 (2016).
Gallinari, P., Marco, S. D., Jones, P., Pallaoro, M. & Steinkühler, C. HDACs, histone deacetylation and gene transcription: from molecular biology to cancer therapeutics. Cell Res. 17, 195–211 (2007).
Lan, F., Nottke, A. C. & Shi, Y. Mechanisms involved in the regulation of histone lysine demethylases. Curr. Opin. Cell Biol. 20, 316–325 (2008).
Torres, I. O. et al. Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism. Nat. Commun. 6, 6204 (2015).
Klein, B. J. et al. The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers. Cell Rep. 6, 325–335 (2014).
Lukasak, B. J. et al. A genetically encoded approach for breaking chromatin symmetry. ACS Cent. Sci. 8, 176–183 (2022). This study describes a practical approach to preparing nucleosomes with asymmetrically modified H3 that is useful for interrogating the reaction of writers and erasers such as KDM5 to nucleosome asymmetry.
Choudhury, R., Singh, S., Arumugam, S., Roguev, A. & Stewart, A. F. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev. 33, 550–564 (2019).
Gatchalian, J. et al. Chromatin condensation and recruitment of PHD finger proteins to histone H3K4me3 are mutually exclusive. Nucleic Acids Res. 44, 6102–6112 (2016).
Farrelly, L. A. et al. Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3. Nature 567, 535–539 (2019).
Zhao, S. et al. Histone H3Q5 serotonylation stabilizes H3K4 methylation and potentiates its readout. Proc. Natl Acad. Sci. USA 118, e2016742118 (2021).
Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492 (2012).
Li, Y., Chen, X. & Lu, C. The interplay between DNA and histone methylation: molecular mechanisms and disease implications. EMBO Rep. 22, e51803 (2021).
Dhayalan, A. et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J. Biol. Chem. 285, 26114–26120 (2010).
Baubec, T. et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 520, 243–247 (2015).
Weinberg, D. N. et al. The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Nature 573, 281–286 (2019).
Kurotaki, N. et al. Haploinsufficiency of NSD1 causes Sotos syndrome. Nat. Genet. 30, 365–366 (2002).
Choufani, S. et al. NSD1 mutations generate a genome-wide DNA methylation signature. Nat. Commun. 6, 10207 (2015).
Sendzikaite, G., Hanna, C. W., Stewart-Morgan, K. R., Ivanova, E. & Kelsey, G. A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice. Nat. Commun. 10, 1884 (2019).
Heyn, P. et al. Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions. Nat. Genet. 51, 96–105 (2019).
Weinberg, D. N. et al. Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands. Nat. Genet. 53, 794–800 (2021). Through a combination of genomic experiments and in vitro nucleosome binding assays, this study shows that DNMT3A recruitment to PRC1-targeted CpG islands is mediated by its N-terminal ubiquitin-dependent recruitment region, which binds H2AK119ub.
Dhalluin, C. et al. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399, 491–496 (1999).
Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000).
Turner, B. M. Decoding the nucleosome. Cell 75, 5–8 (1993).
Schreiber, S. L. & Bernstein, B. E. Signaling network model of chromatin. Cell 111, 771–778 (2002).
Talbert, P. B. & Henikoff, S. The yin and yang of histone marks in transcription. Annu. Rev. Genomics Hum. Genet. 22, 147–170 (2021).
Swygert, S. G. & Peterson, C. L. Chromatin dynamics: interplay between remodeling enzymes and histone modifications. Biochim. Biophys. Acta 1839, 728–736 (2014).
Kim, J. J., Lee, S. Y. & Miller, K. M. Preserving genome integrity and function: the DNA damage response and histone modifications. Crit. Rev. Biochem. Mol. Biol. 54, 208–241 (2019).
Aebersold, R. & Mann, M. Mass-spectrometric exploration of proteome structure and function. Nature 537, 347–355 (2016).
Vermeulen, M. et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58–69 (2007).
Lauberth, S. M. et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 152, 1021–1036 (2013).
Wang, H. et al. H3K4me3 regulates RNA polymerase II promoter-proximal pause-release. Nature 615, 339–348 (2023).
Vermeulen, M. et al. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142, 967–980 (2010).
Zhang, Z. et al. Photo-cross-linking to delineate epigenetic interactome. J. Am. Chem. Soc. 144, 20979–20997 (2022).
Moyle, P. M. & Muir, T. W. Method for the synthesis of mono-ADP-ribose conjugated peptides. J. Am. Chem. Soc. 132, 15878–15880 (2010).
Li, X. & Kapoor, T. M. Approach to profile proteins that recognize post-translationally modified histone “tails”. J. Am. Chem. Soc. 132, 2504–2505 (2010).
Kleiner, R. E., Verma, P., Molloy, K. R., Chait, B. T. & Kapoor, T. M. Chemical proteomics reveals a gammaH2AX-53BP1 interaction in the DNA damage response. Nat. Chem. Biol. 11, 807–814 (2015).
Bao, X. et al. Identification of ‘erasers’ for lysine crotonylated histone marks using a chemical proteomics approach. eLife 3, e02999 (2014).
Lee, K. & O’Reilly, F. J. Cross-linking mass spectrometry for mapping protein complex topologies in situ. Essays Biochem. 67, 215–228 (2023).
Lin, J., Bao, X. & Li, X. D. A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions. Mol. Cell 81, 2669–2681.e9 (2021).
Ruthenburg, A. J., Li, H., Patel, D. J. & Allis, C. D. Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 8, 983–994 (2007).
Bartke, T. et al. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143, 470–484 (2010).
Brustel, J. et al. Histone H4K20 tri-methylation at late-firing origins ensures timely heterochromatin replication. EMBO J. 36, 2726–2741 (2017).
Makowski, M. M. et al. Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry. Nat. Commun. 9, 1653 (2018).
Skrajna, A. et al. Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. Nucleic Acids Res. 48, 9415–9432 (2020).
Spangler, C. J. et al. Structural basis of paralog-specific KDM2A/B nucleosome recognition. Nat. Chem. Biol. 19, 624–632 (2023).
Local, A. et al. Identification of H3K4me1-associated proteins at mammalian enhancers. Nat. Genet. 50, 73–82 (2018).
Nakamura, K. et al. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nat. Cell Biol. 21, 311–318 (2019).
Lin, J. et al. Menin “reads” H3K79me2 mark in a nucleosomal context. Science 379, 717–723 (2023). This study uses a photoaffinity nucleosome probe to capture H3K79me2-specific binders in nuclear extracts, identifying menin as a reader of this PTM; ChIP–seq experiments validate this interaction on native chromatin.
Hughes, C. M. et al. Menin associates with a trithorax family histone methyltransferase complex and with the Hoxc8 locus. Mol. Cell 13, 587–597 (2004).
Wilkins, B. J. et al. A cascade of histone modifications induces chromatin condensation in mitosis. Science 343, 77–80 (2014).
Kleiner, R. E., Hang, L. E., Molloy, K. R., Chait, B. T. & Kapoor, T. M. A chemical proteomics approach to reveal direct protein-protein interactions in living cells. Cell Chem. Biol. 25, 110–120.e3 (2018).
Qin, F. F. et al. Linking chromatin acylation mark-defined proteome and genome in living cells. Cell 186, 1066–1085 (2023). This study uses genetic code expansion to install acylated lysine photoaffinity probes into histones, allowing the capture of mark-specific readers in living cells.
Fang, R. et al. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol. Cell 49, 558–570 (2013).
Burton, A. J. et al. In situ chromatin interactomics using a chemical bait and trap approach. Nat. Chem. 12, 520–527 (2020).
David, Y., Vila-Perello, M., Verma, S. & Muir, T. W. Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat. Chem. 7, 394–402 (2015).
Franklin, K. A., Shields, C. E. & Haynes, K. A. Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering. Trends Biochem. Sci. 47, 417–432 (2022).
Qin, W., Cho, K. F., Cavanagh, P. E. & Ting, A. Y. Deciphering molecular interactions by proximity labeling. Nat. Methods 18, 133–143 (2021).
Villaseñor, R. et al. ChromID identifies the protein interactome at chromatin marks. Nat. Biotechnol. 38, 728–736 (2020).
Santos-Barriopedro, I., van Mierlo, G. & Vermeulen, M. Off-the-shelf proximity biotinylation for interaction proteomics. Nat. Commun. 12, 5015 (2021).
Seath, C. P. et al. Tracking chromatin state changes using nanoscale photo-proximity labelling. Nature 616, 574–580 (2023). This study describes a method for incorporating light-induced proximity labelling catalysts into chromatin, enabling the detection of interactome changes affected by cancer-associated histone mutations.
Geri, J. B. et al. Microenvironment mapping via Dexter energy transfer on immune cells. Science 367, 1091–1097 (2020).
Hananya, N., Ye, X., Koren, S. & Muir, T. W. A genetically encoded photoproximity labeling approach for mapping protein territories. Proc. Natl Acad. Sci. USA 120, e2219339120 (2023).
Zhai, Y. et al. Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling. Nat. Commun. 13, 4906 (2022).
Allis, C. D. & Muir, T. W. Spreading chromatin into chemical biology. Chembiochem 12, 264–279 (2011).
Thompson, R. E. & Muir, T. W. Chemoenzymatic semisynthesis of proteins. Chem. Rev. 120, 3051–3126 (2020).
Meek, D. W. & Anderson, C. W. Posttranslational modification of p53: cooperative integrators of function. Cold Spring Harb. Perspect. Biol. 1, a000950 (2009).
Chen, L., Liu, S. & Tao, Y. Regulating tumor suppressor genes: post-translational modifications. Signal Transduct. Target. Ther. 5, 90 (2020).
Margiola, S., Gerecht, K. & Müller, M. M. Semisynthetic ‘designer’ p53 sheds light on a phosphorylation–acetylation relay. Chem. Sci. 12, 8563–8570 (2021).
Karukurichi, K. R. et al. Analysis of p300/CBP histone acetyltransferase regulation using circular permutation and semisynthesis. J. Am. Chem. Soc. 132, 1222–1223 (2010).
Policarpi, C., Dabin, J. & Hackett, J. A. Epigenetic editing: dissecting chromatin function in context. Bioessays 43, 2000316 (2021).
Nakamura, M., Gao, Y., Dominguez, A. A. & Qi, L. S. CRISPR technologies for precise epigenome editing. Nat. Cell Biol. 23, 11–22 (2021).
Liu, C. C. & Schultz, P. G. Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413–444 (2010).
Nguyen, D. P., Garcia Alai, M. M., Kapadnis, P. B., Neumann, H. & Chin, J. W. Genetically encoding Nε-methyl-L-lysine in recombinant histones. J. Am. Chem. Soc. 131, 14194–14195 (2009).
Neumann, H. et al. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol. Cell 36, 153–163 (2009).
Kim, C. H., Kang, M., Kim, H. J., Chatterjee, A. & Schultz, P. G. Site-specific incorporation of ε-N-crotonyllysine into histones. Angew. Chem. Int. Ed. 51, 7246–7249 (2012).
Lee, S. et al. A facile strategy for selective incorporation of phosphoserine into histones. Angew. Chem. Int. Ed. 52, 5771–5775 (2013).
Simon, M. D. et al. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell 128, 1003–1012 (2007).
Li, F. et al. A direct method for site-specific protein acetylation. Angew. Chem. Int. Ed. 50, 9611–9614 (2011).
Chatterjee, C., McGinty, R. K., Fierz, B. & Muir, T. W. Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation. Nat. Chem. Biol. 6, 267–269 (2010).
Morgan, M. T. et al. Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science 351, 725–728 (2016).
Le, D. D., Cortesi, A. T., Myers, S. A., Burlingame, A. L. & Fujimori, D. G. Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J. Am. Chem. Soc. 135, 2879–2882 (2013).
Dadová, J., Galan, S. R. G. & Davis, B. G. Synthesis of modified proteins via functionalization of dehydroalanine. Curr. Opin. Chem. Biol. 46, 71–81 (2018).
Fu, X.-P. et al. Stereoretentive post-translational protein editing. ACS Cent. Sci. 9, 405–416 (2023).
Josephson, B. et al. Light-driven post-translational installation of reactive protein side chains. Nature 585, 530–537 (2020).
Dawson, P. E., Muir, T. W., Clark-Lewis, I. & Kent, S. B. Synthesis of proteins by native chemical ligation. Science 266, 776–779 (1994).
Maity, S. K., Jbara, M., Mann, G., Kamnesky, G. & Brik, A. Total chemical synthesis of histones and their analogs, assisted by native chemical ligation and palladium complexes. Nat. Protoc. 12, 2293–2322 (2017).
Qi, Y. K., Ai, H. S., Li, Y. M. & Yan, B. Total chemical synthesis of modified histones. Front. Chem. 6, 19 (2018).
Muir, T. W., Sondhi, D. & Cole, P. A. Expressed protein ligation: a general method for protein engineering. Proc. Natl Acad. Sci. USA 95, 6705–6710 (1998).
Muir, T. W. Semisynthesis of proteins by expressed protein ligation. Annu. Rev. Biochem. 72, 249–289 (2003).
Holt, M. & Muir, T. Application of the protein semisynthesis strategy to the generation of modified chromatin. Annu. Rev. Biochem. 84, 265–290 (2015).
Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001).
Szymczak, L. C., Kuo, H.-Y. & Mrksich, M. Peptide arrays: development and application. Anal. Chem. 90, 266–282 (2018).
Matthews, A. G. W. et al. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450, 1106–1110 (2007).
Moreno-Yruela, C. et al. Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases. Nat. Commun. 12, 62 (2021).
Garske, A. L. et al. Combinatorial profiling of chromatin binding modules reveals multisite discrimination. Nat. Chem. Biol. 6, 283–290 (2010).
Morrison, E. A., Bowerman, S., Sylvers, K. L., Wereszczynski, J. & Musselman, C. A. The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome. eLife 7, e31481 (2018).
Dann, G. P. et al. ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference. Nature 548, 607–611 (2017).
Nguyen, U. T. T. et al. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat. Methods 11, 834–840 (2014).
Liszczak, G., Diehl, K. L., Dann, G. P. & Muir, T. W. Acetylation blocks DNA damage–induced chromatin ADP-ribosylation. Nat. Chem. Biol. 14, 837–840 (2018).
Mashtalir, N. et al. Chromatin landscape signals differentially dictate the activities of mSWI/SNF family complexes. Science 373, 306–315 (2021).
Bagert, J. D. et al. Oncohistone mutations enhance chromatin remodeling and alter cell fates. Nat. Chem. Biol. 17, 403–411 (2021).
Jain, K. et al. An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability. eLife 12, e82596 (2023).
Acknowledgements
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.
Author information
Authors and Affiliations
Contributions
The authors contributed equally to all aspects of the article.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
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.
Additional information
This Review is dedicated to the memory of C. David Allis.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Glossary
- 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.
- Epigenetic
-
Heritable gene regulatory information that is not linked to changes in DNA sequence.
- Eraser
-
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).
- Interactome
-
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.
- Reader
-
A protein that binds specifically to post-translationally-modified histones, thereby mediating the post-translational modification’s biological outcome.
- Writer
-
An enzyme that adds modifications to histones or DNA.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Hananya, N., Koren, S. & Muir, T.W. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet 25, 255–271 (2024). https://doi.org/10.1038/s41576-023-00664-z
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41576-023-00664-z
