Skip to main content
SpringerLink
Log in

Cleavage Under Targets & Release Using Nuclease (CUT&RUN) of Histone Modifications in Epidermal Stem Cells of Adult Murine Skin

  • Protocol
  • First Online:
Stem Cells and Lineage Commitment

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2736))

  • 359 Accesses

Abstract

Cleavage Under Targets & Release Using Nuclease (CUT&RUN) has swiftly become the preferred procedure over the past few years for genomic mapping and detecting interactions between chromatin and its bound proteins. CUT&RUN is now being widely used for characterizing the epigenetic landscape in many cell types as it utilizes far less cell numbers when compared to Chromatin Immunoprecipitation-sequencing (ChIP-seq), thereby making it a powerful tool for researchers working with limited material. This protocol has been specifically optimized for detecting histone modifications in fluorescence-activated cell sorting (FACS)-isolated epidermal stem cells from adult mice.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 179.99
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

References

  1. Chen Z, Li S, Subramaniam S, Shyy JYJ, Chien S (2017) Epigenetic regulation: a new frontier for biomedical engineers. Annu Rev Biomed Eng 19(1):195–219

    Article  CAS  PubMed  Google Scholar 

  2. Farrelly LA, Thompson RE, Zhao S, Lepack AE, Lyu Y, Bhanu NV et al (2019) Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3. Nature 567(7749):535–539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Cubeñas-Potts C, Matunis MJ (2013) SUMO: a multifaceted modifier of chromatin structure and function. Dev Cell 24(1):1–12

    Article  PubMed  PubMed Central  Google Scholar 

  4. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41–45

    Article  CAS  PubMed  Google Scholar 

  5. Gelato KA, Fischle W (2008) Role of histone modifications in defining chromatin structure and function. Biol Chem 389(4):353–363

    Article  CAS  PubMed  Google Scholar 

  6. Kouzarides T (2007) Chromatin modifications and their function. Cell 128(4):693–705

    Article  CAS  PubMed  Google Scholar 

  7. Hemberger M, Dean W, Reik W (2009) Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington’s canal. Nat Rev Mol Cell Biol 10(8):526–537

    Article  CAS  PubMed  Google Scholar 

  8. Jambhekar A, Dhall A, Shi Y (2019) Roles and regulation of histone methylation in animal development. Nat Rev Mol Cell Biol 20(10):625–641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Flora P, Ezhkova E (2020) Regulatory mechanisms governing epidermal stem cell function during development and homeostasis. Dev Camb Engl 147(22):dev194100

    CAS  Google Scholar 

  10. Park PJ (2009) ChIP-Seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Skene PJ, Henikoff S (2017) An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6:e21856

    Article  PubMed  PubMed Central  Google Scholar 

  12. Fuchs E (2016) Epithelial skin biology: three decades of developmental biology, a hundred questions answered and a thousand new ones to address. Curr Top Dev Biol 116:357–374

    Article  PubMed  PubMed Central  Google Scholar 

  13. Fuchs E (2018) Skin stem cells in silence, action, and cancer. Stem Cell Rep 10(5):1432–1438

    Article  CAS  Google Scholar 

  14. Moltrasio C, Romagnuolo M, Marzano AV (2022) Epigenetic mechanisms of epidermal differentiation. Int J Mol Sci 23(9):4874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Katiyar SK, Singh T, Prasad R, Sun Q, Vaid M (2012) Epigenetic alterations in ultraviolet radiation-induced skin carcinogenesis: interaction of bioactive dietary components on epigenetic targets. Photochem Photobiol 88(5):1066–1074

    Article  CAS  PubMed  Google Scholar 

  16. Shen Y, Stanislauskas M, Li G, Zheng D, Liu L (2017) Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses. Sci Rep 7(1):42646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Li MY, Flora P, Pu H, Bar C, Silva J, Cohen I et al (2021) UV-induced reduction in Polycomb repression promotes epidermal pigmentation. Dev Cell 56(18):2547–2561.e8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Rheinwald JG, Green H (1977) Epidermal growth factor and the multiplication of cultured human epidermal keratinocytes. Nature 265(5593):421–424

    Article  CAS  PubMed  Google Scholar 

  19. Meers MP, Bryson TD, Henikoff JG, Henikoff S (2019) Improved CUT&RUN chromatin profiling tools. Parker S, Weigel D, editors. eLife 8:e46314

    Article  PubMed  PubMed Central  Google Scholar 

  20. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Orlando DA, Chen MW, Brown VE, Solanki S, Choi YJ, Olson ER et al (2014) Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep 9(3):1163–1170

    Article  CAS  PubMed  Google Scholar 

  22. Tay RE, Olawoyin O, Cejas P, Xie Y, Meyer CA, Ito Y et al (2020) Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. J Exp Med 217(7):e20191453

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G et al (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by NIH grants P30 AR079200 and R01 AR069078 awarded to E.E.

Author information

Authors and Affiliations

  1. Black Family Stem Cell Institute, Department of Cell Development and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Pooja Flora & Elena Ezhkova

Authors
  1. Pooja Flora
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Elena Ezhkova
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Elena Ezhkova .

Editor information

Editors and Affiliations

  1. Ottawa, ON, Canada

    Kursad Turksen

Rights and permissions

Reprints and permissions

Copyright information

© 2023 Springer Science+Business Media, LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Flora, P., Ezhkova, E. (2023). Cleavage Under Targets & Release Using Nuclease (CUT&RUN) of Histone Modifications in Epidermal Stem Cells of Adult Murine Skin. In: Turksen, K. (eds) Stem Cells and Lineage Commitment. Methods in Molecular Biology, vol 2736. Humana, New York, NY. https://doi.org/10.1007/7651_2023_499

Download citation

  • DOI: https://doi.org/10.1007/7651_2023_499

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3536-0

  • Online ISBN: 978-1-0716-3537-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation