Skip to main content
SpringerLink
Log in

Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture

  • Protocol
  • First Online:
Plant Chromatin Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1675))

Abstract

The introduction of chromosome conformation capture (3C) technologies boosted the field of 3D-genome research and significantly enhanced the available toolset to study chromosomal architecture. 3C technologies not only offer increased resolution compared to the previously dominant cytological approaches but also allow the simultaneous study of genome-wide 3D chromatin contacts, thereby enabling a candidate-free perspective on 3D-genome architecture. Since its introduction in 2002, 3C technologies evolved rapidly and now constitute a collection of tools, each with their strengths and pitfalls with respect to specific research questions. This chapter aims at guiding 3C novices through the labyrinth of potential applications of the various family members, hopefully providing a valuable basis for choosing the appropriate strategy for different research questions.

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

Access this chapter

Log in via an institution

Institutional subscriptions

References

  1. Hagège H, Klous P, Braem C et al (2007) Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc 2:1722–1733. doi:10.1038/nprot.2007.243

    Article  PubMed  Google Scholar 

  2. Louwers M, Splinter E, van Driel R et al (2009) Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C). Nat Protoc 4:1216–1229. doi:10.1038/nprot.2009.113

    Article  CAS  PubMed  Google Scholar 

  3. Miele A, Dekker J (2008) Mapping cis-and trans-chromatin interaction networks using chromosome conformation capture (3C). In: Hancock R. (ed) The nucleus: volume 2: chromatin, transcription, envelope, proteins, dynamics, and imaging. Methods in molecular biology. Humana, Totowa 464:105–121. doi: 10.1007/978-1-60327-461-6_7

  4. Dekker J (2006) The three “C” s of chromosome conformation capture: controls, controls, controls. Nat Methods 3:17–21. doi:10.1038/nmeth823

    Article  CAS  PubMed  Google Scholar 

  5. Comet I, Schuettengruber B, Sexton T, Cavalli G (2011) A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber. Proc Natl Acad Sci U S A 108:2294–2299. doi:10.1073/pnas.1002059108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Weber B, Jamge S, Stam M (2017) 3C analysis in Maize and Arabidopsis. Methods Mol Biol

    Google Scholar 

  7. Dekker J (2002) Capturing Chromosome Conformation. Science 295:1306–1311. doi:10.1126/science.1067799

    Article  CAS  PubMed  Google Scholar 

  8. Louwers M, Bader R, Haring M et al (2009) Tissue- and expression level-specific chromatin looping at Maize b1 Epialleles. Plant Cell 21:832–842. doi:10.1105/tpc.108.064329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Crevillen P, Sonmez C, Wu Z, Dean C (2012) A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization. EMBO J 32:140–148. doi:10.1038/emboj.2012.324

    Article  PubMed  PubMed Central  Google Scholar 

  10. Ariel F, Jegu T, Latrasse D et al (2014) Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell 55:383–396. doi:10.1016/j.molcel.2014.06.011

    Article  CAS  PubMed  Google Scholar 

  11. Dostie J, Zhan Y, Dekker J (2007) Chromosome conformation capture carbon copy technology. Curr Protoc Mol Biol Chapter 21:Unit 21.14. doi: 10.1002/0471142727.mb2114s80

  12. Dostie J, Dekker J (2007) Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2:988–1002. doi:10.1038/nprot.2007.116

    Article  CAS  PubMed  Google Scholar 

  13. Lajoie BR, van Berkum NL, Sanyal A, Dekker J (2009) My5C: web tools for chromosome conformation capture studies. Nat Methods 6:690–691. doi:10.1038/nmeth1009-690

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Dostie J, Richmond TA, Arnaout RA et al (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16:1299–1309. doi:10.1101/gr.5571506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Sauria ME, Phillips-Cremins JE, Corces VG, Taylor J (2015) HiFive: a tool suite for easy and efficient HiC and 5C data analysis. Genome Biol:1–10. doi:10.1186/s13059-015-0806-y

  16. Simonis M, Klous P, Homminga I et al (2009) High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat Methods 6:837–842. doi:10.1038/nmeth.1391

    Article  CAS  PubMed  Google Scholar 

  17. Grob S, Schmid MW, Luedtke NW et al (2013) Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biol 14:R129. doi:10.1186/gb-2013-14-11-r129

    Article  PubMed  PubMed Central  Google Scholar 

  18. Sexton T, Kurukuti S, Mitchell JA et al (2012) Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip. Nat Protoc 7:1335–1350. doi:10.1038/nprot.2012.071

    Article  CAS  PubMed  Google Scholar 

  19. Grob S (2017) Circular chromosome conformation capture in plants. Methods Mol Biol 1610:73–92. doi:10.1007/978-1-4939-7003-2_6

    Article  PubMed  Google Scholar 

  20. Zhao Z, Tavoosidana G, Sjölinder M et al (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38:1341–1347. doi:10.1038/ng1891

    Article  CAS  PubMed  Google Scholar 

  21. Simonis M, Klous P, Splinter E et al (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348–1354. doi:10.1038/ng1896

    Article  CAS  PubMed  Google Scholar 

  22. van de Werken HJG, Landan G, Holwerda SJB et al (2012) Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods 9:969–972. doi:10.1038/nmeth.2173

    Article  PubMed  Google Scholar 

  23. Klein FA, Pakozdi T, Anders S et al (2015) FourCSeq: analysis of 4C sequencing data. Bioinformatics 31:3085–3091. doi:10.1093/bioinformatics/btv335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Robinson MD, McCarthy DJ, Smyth GK (2009) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. doi:10.1093/bioinformatics/btp616

    Article  PubMed  PubMed Central  Google Scholar 

  25. Grob S, Grossniklaus U (2017) Chromatin Conformation Capture-based analysis of nuclear architecture. Methods Mol Biol 1456:15–32. doi: 10.1007/978-1-4899-7708-3_2

  26. van Berkum NL, Lieberman-Aiden E, Williams L et al (2010) Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp:1–7. doi:10.3791/1869

  27. Kalhor R, Tjong H, Jayathilaka N et al (2011) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol 30:90–98. doi:10.1038/nbt.2057

    Article  PubMed  PubMed Central  Google Scholar 

  28. Belton J-M, McCord RP, Gibcus JH et al (2012) Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58:268–276. doi:10.1016/j.ymeth.2012.05.001

    Article  CAS  PubMed  Google Scholar 

  29. Ramani V, Cusanovich DA, Hause RJ et al (2016) Mapping 3D genome architecture through in situ DNase Hi-C. Nat Protoc 11:2104–2121. doi:10.1038/nprot.2016.126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sexton T, Yaffe E, Kenigsberg E et al (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148:458–472. doi:10.1016/j.cell.2012.01.010

    Article  CAS  PubMed  Google Scholar 

  32. Korbel JO, Lee C (2013) Genome assembly and haplotyping with Hi-C. Nat Biotechnol 31:1099–1101. doi:10.1038/nbt.2764

    Article  CAS  PubMed  Google Scholar 

  33. Kaplan N, Dekker J (2013) High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol 31:1143–1147. doi:10.1038/nbt.2768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Adey A, Patwardhan RP, Qiu R et al (2013) Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 31:1119–1125. doi:10.1038/nbt.2727

    Article  PubMed  PubMed Central  Google Scholar 

  35. Lesne A, Riposo J, Roger P et al (2014) 3D genome reconstruction from chromosomal contacts. Nat Methods 11:1141–1143. doi:10.1038/nmeth.3104

    Article  CAS  PubMed  Google Scholar 

  36. Nagano T, Lubling Y, Stevens TJ et al (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502:59–64. doi:10.1038/nature12593

    Article  CAS  PubMed  Google Scholar 

  37. Feng S, Cokus SJ, Schubert V et al (2014) Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell 55:694–707. doi:10.1016/j.molcel.2014.07.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Grob S, Schmid MW, Grossniklaus U (2014) Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila. Mol Cell 55:678–693. doi:10.1016/j.molcel.2014.07.009

    Article  CAS  PubMed  Google Scholar 

  39. Wang C, Liu C, Roqueiro D et al (2014) Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res 25:246–256. doi:10.1101/gr.170332.113

    Article  PubMed  Google Scholar 

  40. Liu C, Wang C, Wang G et al (2016) Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution. Genome Res 26:1057–1068. doi:10.1101/gr.204032.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Moissiard G, Cokus SJ, Cary J et al (2012) MORC family ATPases required for heterochromatin condensation and gene silencing. Science 336:1448–1451. doi:10.1126/science.1221472

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Veluchamy A, Jegu T, Ariel F et al (2016) LHP1 regulates H3K27me3 spreading and shapes the three-dimensional conformation of the Arabidopsis Genome. PLoS One 11:e0158936–e0158925. doi:10.1371/journal.pone.0158936

    Article  PubMed  PubMed Central  Google Scholar 

  43. Fullwood MJ, Han Y, Wei C-L et al (2010) Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol Chapter 21:Unit 21.15.1–25. doi: 10.1002/0471142727.mb2115s89

  44. Goh Y, Fullwood MJ, Poh HM et al (2012) Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation. J Vis Exp. doi: 10.3791/3770

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Fullwood MJ, Liu MH, Pan YF et al (2009) An oestrogen-receptor-α-bound human chromatin interactome. Nature 461:58–64. doi:10.1038/nature08497

    Article  Google Scholar 

  47. 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. doi:10.1101/gr.175034.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kolovos P, van de Werken HJ, Kepper N et al (2014) Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics Chromatin 7:10–17. doi:10.1186/1756-8935-7-10

    Article  PubMed  PubMed Central  Google Scholar 

  49. Mifsud B, Tavares-Cadete F, Young AN et al (2015) Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet 47:598–606. doi:10.1038/ng.3286

    Article  CAS  PubMed  Google Scholar 

  50. Jäger R, Migliorini G, Henrion M et al (2015) Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun 6:6178. doi:10.1038/ncomms7178

    Article  PubMed  PubMed Central  Google Scholar 

  51. Liu C, Weigel D (2015) Chromatin in 3D: progress and prospects for plants. Genome Biol 16:1–6. doi:10.1186/s13059-015-0738-6

    Article  Google Scholar 

  52. Grob S, Grossniklaus U (2017) Chromosome Conformation Capture-based studies reveal novel features of plant nuclear architecture. Curr Opin Plant Biol 36:149–157

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Human Genetics, Centre National de la Recherche UMR9002, Montpellier, France

    Stefan Grob & Giacomo Cavalli

Authors
  1. Stefan Grob
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Giacomo Cavalli
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Stefan Grob .

Editor information

Editors and Affiliations

  1. Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

    Marian Bemer

  2. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

    Célia Baroux

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Grob, S., Cavalli, G. (2018). Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture. In: Bemer, M., Baroux, C. (eds) Plant Chromatin Dynamics. Methods in Molecular Biology, vol 1675. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7318-7_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7318-7_14

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7317-0

  • Online ISBN: 978-1-4939-7318-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation