Skip to main content

Using ChIP-SICAP to Identify Proteins That Co-localize in Chromatin

  • Protocol
  • First Online:
Enhancers and Promoters

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2351))

Abstract

Functionalization of the genome is carried out by proteins that bind to DNA to regulate gene expression. Since this process is highly dynamic, context-dependent, and rarely performed by single proteins alone, we here describe ChIP-SICAP to identify proteins that co-localize with a protein of interest on the genome. Benefiting from its nature as a dual purification approach via ChIP and DNA biotinylation, ChIP-SICAP distinguishes genuine chromatin-binders and is uniquely placed to identify novel players in genome regulation.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
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. Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53(6):937–947. https://doi.org/10.1016/s0092-8674(88)90469-2

    Article  CAS  PubMed  Google Scholar 

  2. Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI (2013) Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 20(2):202–209. https://doi.org/10.1038/nsmb.2477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Lambert JP, Tucholska M, Pawson T, Gingras AC (2014) Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners. J Proteome 100:55–59. https://doi.org/10.1016/j.jprot.2013.12.022

    Article  CAS  Google Scholar 

  4. Ohta S, Bukowski-Wills JC, Sanchez-Pulido L, Alves Fde L, Wood L, Chen ZA, Platani M, Fischer L, Hudson DF, Ponting CP, Fukagawa T, Earnshaw WC, Rappsilber J (2010) The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. Cell 142(5):810–821. https://doi.org/10.1016/j.cell.2010.07.047

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J (2016) Expanding the circuitry of pluripotency by selective isolation of chromatin-associated proteins. Mol Cell 64(3):624–635. https://doi.org/10.1016/j.molcel.2016.09.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Rafiee MR, Sigismondo G, Kalxdorf M, Forster L, Brugger B, Bethune J, Krijgsveld J (2020) Protease-resistant streptavidin for interaction proteomics. Mol Syst Biol 16(5):e9370. https://doi.org/10.15252/msb.20199370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Mahmoud-Reza Rafiee or Jeroen Krijgsveld .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 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

Rafiee, MR., Krijgsveld, J. (2021). Using ChIP-SICAP to Identify Proteins That Co-localize in Chromatin. In: Borggrefe, T., Giaimo, B.D. (eds) Enhancers and Promoters. Methods in Molecular Biology, vol 2351. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1597-3_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1597-3_15

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1596-6

  • Online ISBN: 978-1-0716-1597-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics