Skip to main content

Capturing Chromosome Conformation

  • Protocol
  • First Online:
Capturing Chromosome Conformation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2157))

Abstract

The genome is organized in 3D topology-associated domains to ensure proper gene transcriptional processes. The chromosome conformation capture (3C) is an affordable method to investigate local chromatin structure and dynamics in cells and tissue. Herein I describe an easy to design and a cost-effective protocol.

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 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. Merkenschlager M, Nora EP (2016) CTCF and Cohesin in genome folding and transcriptional gene regulation. Annu Rev Genomics Hum Genet 17:17–43

    Article  CAS  Google Scholar 

  2. Rowley MJ, Corces VG (2018) Organizational principles of 3D genome architecture. Nat Rev Genet 19(12):789–800

    Article  CAS  Google Scholar 

  3. Moore-Morris T et al (2018) Role of epigenetics in cardiac development and congenital diseases. Physiol Rev 98(4):2453–2475

    Article  Google Scholar 

  4. Dekker J (2006) The three ‘C’ s of chromosome conformation capture: controls, controls, controls. Nat Methods 3(1):17–21

    Article  CAS  Google Scholar 

  5. Ea V, Court F, Forne T (2017) Quantitative analysis of intra-chromosomal contacts: the 3C-qPCR method. Methods Mol Biol 1589:75–88

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  7. van de Werken HJ et al (2012) Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods 9(10):969–972

    Article  Google Scholar 

  8. Flyamer IM et al (2017) Single-nucleus hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature 544(7648):110–114

    Article  CAS  Google Scholar 

  9. Nagano T et al (2017) Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547(7661):61–67

    Article  CAS  Google Scholar 

  10. Grob S, Cavalli G (2018) Technical review: a Hitchhiker’s guide to chromosome conformation capture. Methods Mol Biol 1675:233–246

    Article  CAS  Google Scholar 

  11. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45

    Google Scholar 

  12. Abboud N et al (2015) A cohesin-OCT4 complex mediates Sox enhancers to prime an early embryonic lineage. Nat Commun 6:6749

    Article  CAS  Google Scholar 

  13. Bintu B et al (2018) Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362:6413

    Article  Google Scholar 

  14. Zheng M et al (2019) Multiplex chromatin interactions with single-molecule precision. Nature 566(7745):558–562

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Michel Pucéat .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Pucéat, M. (2021). Capturing Chromosome Conformation. In: Bodega, B., Lanzuolo, C. (eds) Capturing Chromosome Conformation. Methods in Molecular Biology, vol 2157. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0664-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0664-3_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0663-6

  • Online ISBN: 978-1-0716-0664-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics