Skip to main content
SpringerLink
Log in

Chromatin Immunoprecipitation of Skeletal Muscle Tissue

  • Protocol
  • First Online:
Chromatin Immunoprecipitation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1689))

Abstract

Chromatin immunoprecipitation (ChIP) is an invaluable method for studying interactions between histone proteins and genomic DNA regions and transcriptional regulation using antibodies to enrich genomic regions associated with these epitopes. Either to monitor the presence of histones with post-translational modifications at specific genomic locations or to measure transcription factor interactions with a candidate target gene, protein–DNA complexes are most commonly crosslinked using formaldehyde, which stabilizes these transient interactions. Chromatin is then fragmented to allow separation of genomic fragments bound by the histone or transcription factor of interest away from those that are unbound. Following immunoprecipitation, formaldehyde crosslinks are reversed and enriched DNA fragments are purified. While some investigators have successfully performed ChIP experiments from crosslinked skeletal muscle in cell culture, the process is relatively inefficient compared to whole tissue. This chapter provides protocols specifically designed for the crosslinking and immunoprecipitation of human skeletal muscle biopsy samples in preparation for chromatin immunoprecipitation-sequencing (ChIP-seq).

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 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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. Saini A, Mastana S, Myers F et al (2013) ‘From death, lead me to immortality’–mantra of ageing skeletal muscle. Curr Genomics 14:256–267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Consortium EP, Birney E, Stamatoyannopoulos JA et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816

    Article  Google Scholar 

  3. Koch CM, Andrews RM, Flicek P et al (2007) The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res 17:691–707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Krivtsov AV, Feng Z, Lemieux ME et al (2008) H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell 14:355–368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Groth A, Rocha W, Verreault A et al (2007) Chromatin challenges during DNA replication and repair. Cell 128:721–733

    Article  CAS  PubMed  Google Scholar 

  6. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080

    Article  CAS  PubMed  Google Scholar 

  7. Massie CE, Mills IG (2011) Global identification of androgen response elements. Methods Mol Biol 776:255–273

    Article  CAS  PubMed  Google Scholar 

  8. Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25:99–104

    Article  CAS  PubMed  Google Scholar 

  9. Carey MF, Peterson CL, Smale ST (2009) Chromatin immunoprecipitation (ChIP). Cold Spring Harb Protoc 2009:pdbprot5279

    Google Scholar 

  10. Ohkawa Y, Mallappa C, Vallaster CS et al (2012) Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays. Methods Mol Biol 798:517–530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Wells J, Farnham PJ (2002) Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 26:48–56

    Article  CAS  PubMed  Google Scholar 

  12. Thorne AW, Myers FA, Hebbes TR (2004) Native chromatin immunoprecipitation. Methods Mol Biol 287:21–44

    CAS  PubMed  Google Scholar 

  13. Das PM, Ramachandran K, vanWert J et al (2004) Chromatin immunoprecipitation assay. BioTechniques 37:961–969

    CAS  PubMed  Google Scholar 

  14. Mejat A, Ramond F, Bassel-Duby R et al (2005) Histone deacetylase 9 couples neuronal activity to muscle chromatin acetylation and gene expression. Nat Neurosci 8:313–321

    Article  CAS  PubMed  Google Scholar 

  15. Liu ET, Pott S, Huss M (2010) Q&A: ChIP-seq technologies and the study of gene regulation. BMC Biol 8:56

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Burden DW (2012) Guide to the disruption of biological samples. Random Primers 12:1–25

    Google Scholar 

  17. Tian B, Yang J, Brasier AR (2012) Two-step cross-linking for analysis of protein-chromatin interactions. Methods Mol Biol 809:105–120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Crane-Robinson C, Myers FA, Hebbes TR et al (1999) Chromatin immunoprecipitation assays in acetylation mapping of higher eukaryotes. Methods Enzymol 304:533–547

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Patrick Muller at BEA—the core facility for Bioinformatics and Expression Analysis—Karolinska Institutet, Huddinge for quantifying ChIP enrichments and mapping ChIP-enriched genomic DNA fragments to the genome using ChIP-seq as well as help with editing the protocol.We thank Fiona Myers at the School of Biological Sciences, University of Portsmouth for her scientific advice and extensive knowledge in XChIP, NChIP, ChIP-seq and help with editing the protocol.

Author information

Authors and Affiliations

  1. Department of Laboratory Medicine, Clinical Physiology Karolinska Institutet and Unit of Clinical Physiology, Karolinska University Hospital, 141 86, Stockholm, Sweden

    Amarjit Saini & Carl Johan Sundberg

  2. Molecular Exercise Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden

    Carl Johan Sundberg

  3. Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, 171 77, Stockholm, Sweden

    Carl Johan Sundberg

Authors
  1. Amarjit Saini
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carl Johan Sundberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Amarjit Saini .

Editor information

Editors and Affiliations

  1. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

    Neus Visa

  2. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

    Antonio Jordán-Pla

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Saini, A., Sundberg, C.J. (2018). Chromatin Immunoprecipitation of Skeletal Muscle Tissue. In: Visa, N., Jordán-Pla, A. (eds) Chromatin Immunoprecipitation. Methods in Molecular Biology, vol 1689. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7380-4_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7380-4_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7379-8

  • Online ISBN: 978-1-4939-7380-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation