Skip to main content

Preparation and Characterization of Chromatin Templates for Histone Methylation Assays

  • Protocol
  • First Online:
Histone Methyltransferases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2529))

Abstract

In eukaryotic cells, chromatin plays an important role in gene regulation by controlling the access of the transcription machinery to DNA. In this chapter, we will describe methods for generating different chromatin templates to investigate the impact of histone variants and chromatin structure on histone methyltransferase activities. For this purpose, we take Polycomb Repressive Complex 2 (PRC2) as an example and investigate how its activity on H3K27me3 is regulated by the histone variants H3.3 and H2A.Z and higher-order chromatin structure.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Chen P, Li G (2010) Dynamics of the higher-order structure of chromatin. Protein Cell 1:967–971

    Google Scholar 

  2. Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G (2009) H3.3/H2A.Z double variant-containing nucleosomes mark nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet 41:941–945

    Article  CAS  Google Scholar 

  3. Talbert PB, Henikoff S (2010) Histone variants — ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 11:264–275

    Article  CAS  Google Scholar 

  4. Long H, Zhang L, Lv M, Wen Z, Zhang W, Chen X, Zhang P, Li T, Chang L, Jin C (2020) H2A.Z facilitates licensing and activation of early replication origins. Nature 577:576–581

    Article  CAS  Google Scholar 

  5. Wang Y, Long H, Yu J, Dong L, Wassef M, Zhuo B, Li X, Zhao J, Wang M, Liu C, Wen Z, Chang L, Chen P, Wang Q, Xu X, Margueron R, Li G (2018) Histone variants H2A.Z and H3.3 coordinately regulate PRC2-dependent H3K27me3 deposition and gene expression regulation in mES cells. BMC Biol 16(107)

    Google Scholar 

  6. Chen P, Zhao J, Wang Y, Wang M, Long H, Liang D, Huang L, Wen Z, Li W, Li X (2013) H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev 27:2109–2124

    Article  CAS  Google Scholar 

  7. Park YJ, Dyer PN, Tremethick DJ, Luger K (2004) A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome. J Biol Chem 279:24274–24282

    Article  CAS  Google Scholar 

  8. Hoch DA, Stratton JJ, Gloss LM (2007) Protein–protein frster resonance energy transfer analysis of nucleosome core particles containing H2A and H2A.Z. J Mol Biol 371:971–988

    Article  CAS  Google Scholar 

  9. Jin C, Felsenfeld G (2007) Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 21:1519–1529

    Article  CAS  Google Scholar 

  10. Thakar A, Gupta P, Ishibashi T, Finn R, Silva-Moreno B, Uchiyama S, Fukui K, Tomschik M, Ausio J, Zlatanova J (2009) H2A.Z and H3.3 histone variants affect nucleosome structure: biochemical and biophysical studies. Biochemistry 48:10852–10857

    Article  CAS  Google Scholar 

  11. Creyghton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, Young RA, Jaenisch R, Boyer LA (2008) H2AZ is enriched at Polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 135:649–661

    Article  CAS  Google Scholar 

  12. Banaszynski L, Wen D, Dewell S, Whitcomb S, Lin M, Diaz N, Elssser S, Chapgier A, Goldberg A, Canaani E, Rafii S, Zheng D, Allis CD (2013) Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155:107–120

    Google Scholar 

  13. Yuan W, Wu T, Fu H, Dai C, Wu H, Liu N, Li X, Xu M, Zhang Z, Niu T (2012) Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science 337:971–975

    Article  CAS  Google Scholar 

  14. Zhao J, Wang M, Chang L, Yu J, Song A, Liu C, Huang W, Zhang T, Wu X, Shen X et al (2020) RYBP/YAF2-PRC1 complexes and histone H1-dependent chromatin compaction mediate propagation of H2AK119ub1 during cell division. Nat Cell Biol 22:439–452

    Article  CAS  Google Scholar 

  15. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 a resolution. Nature 389:251–260

    Article  CAS  Google Scholar 

  16. He S, Bauman D, Davis JS, Loyola A, Nishioka K, Gronlund JL, Reinberg D, Meng F, Kelleher N, Mccafferty DG (2003) Facile synthesis of site-specifically acetylated and methylated histone proteins: reagents for evaluation of the histone code hypothesis. Proc Natl Acad Sci U S A 100:12033–12038

    Article  CAS  Google Scholar 

  17. Blanco-Canosa J, Dawson P (2007) An efficient Fmoc-SPPS approach for the generation of thioester peptide precursors for use in native chemical ligation. Angew Chem 47:6851–6855

    Article  Google Scholar 

  18. Fierz B, Kilic S, Hieb AR, Luger K, Muir TW (2012) Stability of nucleosomes containing homogenously Ubiquitylated H2A and H2B prepared using Semisynthesis. J Am Chem Soc 134:19548–19551

    Article  CAS  Google Scholar 

  19. Muller MM, Fierz B, Bittova L, Liszczak G, Muir TW (2016) A two-state activation mechanism controls the histone methyltransferase Suv39h1. Nat Chem Biol 12:188–193

    Article  CAS  Google Scholar 

  20. Martin CC, Cao R, Zhang Y (2006) Substrate preferences of the EZH2 histone methyltransferase complex. J Biol Chem 281:8365–8370

    Article  CAS  Google Scholar 

  21. Lu X, Wontakal SN, Kavi H, Kim BJ, Guzzardo PM, Emelyanov AV, Xu N, Hannon GJ, Zavadil J, Fyodorov DV (2013) Drosophila H1 regulates the genetic activity of heterochromatin by recruitment of Su(var)3-9. Science 340:78–81

    Article  CAS  Google Scholar 

  22. Kalb R, Latwiel S, Baymaz HI, Jansen PW, Muller CW, Vermeulen M, Muller J (2014) Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat Struct Mol Biol 21:569–571

    Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the Ministry of Science and Technology of China (2017YFA0504202 to G.L.; 2019YFA0508903 to J.Z.), the National Natural Science Foundation of China (31991161,31521002 to G.L.; 32070604 to J.C.) and the Beijing Municipal Science and Technology Committee (Z201100005320013 to G.L.). The work was also supported by the CAS Key Research Program on Frontier Science (QYZDY-SSW-SMC020 to G.L.), the Chinese Academy of Sciences (CAS) Strategic Priority Research Program (XDB19040202), an HHMI International Research Scholar grant (55008737) to G.L.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Guohong Li .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Liu, C., Zhao, J., Li, G. (2022). Preparation and Characterization of Chromatin Templates for Histone Methylation Assays. In: Margueron, R., Holoch, D. (eds) Histone Methyltransferases. Methods in Molecular Biology, vol 2529. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2481-4_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2481-4_4

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2480-7

  • Online ISBN: 978-1-0716-2481-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics