SpringerLink
Log in

Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq)

  • Protocol
  • First Online:
Enhancers and Promoters

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

Abstract

Proximity ligation-assisted ChIP-Seq (PLAC-Seq), also known as HiChIP, is a method to detect and quantify chromatin contacts anchored at genomic regions bound by specific proteins or histone modifications. By combining in situ Hi-C and chromatin immunoprecipitation (ChIP) using antibodies against transcription factors (TFs) or histone marks of interest, the method achieves targeted interrogation of chromatin organization at a subset of genomic regions. PLAC-Seq is able to identify long-range chromatin interactions at kilobase-scale resolution with significantly reduced sequencing cost.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /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
EUR 44.95
Price includes VAT (Germany)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
EUR 109.99
Price includes VAT (Germany)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
EUR 139.09
Price includes VAT (Germany)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
EUR 192.59
Price includes VAT (Germany)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** 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. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306–1311. https://doi.org/10.1126/science.1067799

    Article  CAS  PubMed  Google Scholar 

  2. Dekker J, Marti-Renom MA, Mirny LA (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 14:390–403. https://doi.org/10.1038/nrg3454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Denker A, de Laat W (2016) The second decade of 3C technologies: detailed insights into nuclear organization. Genes Dev 30:1357–1382. https://doi.org/10.1101/gad.281964.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Schmitt AD, Hu M, Ren B (2016) Genome-wide map** and analysis of chromosome architecture. Nat Rev Mol Cell Biol 17(12):743–755. https://doi.org/10.1038/nrm.2016.104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive map** of long-range interactions reveals folding principles of the human genome. Science 326:289–293. https://doi.org/10.1126/science.1181369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Rao SSP, Huntley MH, Durand NC et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin loo**. Cell 159:1665–1680. https://doi.org/10.1016/j.cell.2014.11.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Fullwood MJ, Liu MH, Pan YF et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64. https://doi.org/10.1038/nature08497

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Dryden NH, Broome LR, Dudbridge F et al (2014) Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res 24:1854–1868. https://doi.org/10.1101/gr.175034.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Hughes JR, Roberts N, McGowan S et al (2014) Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 46:205–212. https://doi.org/10.1038/ng.2871

    Article  CAS  PubMed  Google Scholar 

  10. Mumbach MR, Rubin AJ, Flynn RA et al (2016) HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods 13:919–922. https://doi.org/10.1038/nmeth.3999

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Fang R, Yu M, Li G et al (2016) Map** of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res 26:1345–1348. https://doi.org/10.1038/cr.2016.137

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Juric I, Yu M, Abnousi A et al (2019) MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol 15:e1006982. https://doi.org/10.1371/journal.pcbi.1006982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Landt SG, Marinov GK, Kundaje A et al (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22:1813–1831. https://doi.org/10.1101/gr.136184.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work is supported by U54 DK107977 to B.R.

Author information

Authors and Affiliations

  1. Ludwig Institute for Cancer Research, La Jolla, CA, USA

    Miao Yu & Bing Ren

  2. State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China

    Miao Yu

  3. Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA

    Ivan Juric, Armen Abnousi & Ming Hu

  4. Center for Epigenomics, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA

    Bing Ren

Authors
  1. Miao Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivan Juric
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Armen Abnousi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ming Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Bing Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bing Ren .

Editor information

Editors and Affiliations

  1. Institute of Biochemistry, University of Giessen, Gießen, Hessen, Germany

    Tilman Borggrefe

  2. Institute of Biochemistry, University of Giessen, Gießen, Hessen, Germany

    Benedetto Daniele Giaimo

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

Yu, M., Juric, I., Abnousi, A., Hu, M., Ren, B. (2021). Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). 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_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1597-3_10

  • 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

Search

Navigation