Advertisement

Generation and Analysis of Chromosomal Contact Maps of Bacteria

  • Martial Marbouty
  • Romain Koszul
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1624)

Abstract

This methods article described a protocol aiming at generating chromosome contact maps of bacterial species using a genome-wide derivative of the chromosome conformation capture (3C) technique. The approach is readily applicable on a broad variety of gram + and gram-bacterial species. It describes and addresses known caveats and technicalities associated with the technique, and should be of interest to any laboratory interested to perform a multiscale analysis of the genome structure of its species of interest.

Key words

Chromosome conformation capture, Hi-C 3C Genome organization Nucleoid 

Notes

Acknowledgments

This research was supported by funding to R.K. from the European Research Council under the seventh Framework Program (FP7/2007-2013, ERC grant agreement 260822) and from Agence Nationale pour la Recherche (HiResBaCS ANR-15-CE11-0023).

References

  1. 1.
    Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong S-H et al (2011) The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell 44(2):252–264CrossRefPubMedGoogle Scholar
  2. 2.
    Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295(5558):1306–1311CrossRefPubMedGoogle Scholar
  3. 3.
    Le TBK, Imakaev MV, Mirny LA, Laub MT (2013) High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342(6159):731–734CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Marbouty M, Cournac A, Flot J-F, Marie-Nelly H, Mozziconacci J, Koszul R (2014) Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife 3:e03318CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche J-B et al (2015) Condensin- and replication-mediated bacterial chromosome folding and origin condensation revealed by hi-C and super-resolution imaging. Mol Cell 59(4):588–602CrossRefPubMedGoogle Scholar
  6. 6.
    Val M-E, Marbouty M, de Lemos MF, Kennedy SP, Kemble H, Bland MJ et al (2016) A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae. Sci Adv 2:e150194. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846446/ CrossRefGoogle Scholar
  7. 7.
    Wang X, Le TBK, Lajoie BR, Dekker J, Laub MT, Rudner DZ (2015) Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus Subtilis. Genes Dev 29(15):1661–1675CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Le TB, Laub MT (2016) Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries. EMBO J 35(14):1582–1595CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Gavrilov AA, Gushchanskaya ES, Strelkova O, Zhironkina O, Kireev II, Iarovaia OV et al (2013) Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub. Nucleic Acids Res 41(6):3563–3575CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J (2012) Normalization of a chromosomal contact map. BMC Genomics 13:436CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR et al (2012) Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9(10):999–1003CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Yaffe E, Tanay A (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43(11):1059–1065CrossRefPubMedGoogle Scholar
  14. 14.
    Cournac A, Marbouty M, Mozziconacci J, Koszul R (2016) Generation and analysis of chromosomal contact maps of yeast species. Methods Mol Biol 1361:227–245CrossRefPubMedGoogle Scholar
  15. 15.
    Lajoie BR, Dekker J, Kaplan N (2015) The Hitchhiker’s guide to hi-C analysis: practical guidelines. Methods 72:65–75CrossRefPubMedGoogle Scholar
  16. 16.
    Wingett S, Ewels P, Furlan-Magaril M, Nagano T, Schoenfelder S, Fraser P et al (2015) HiCUP: pipeline for mapping and processing Hi-C data. F1000Res 4:1310. Available from: http://f1000research.com/articles/4-1310/v1 PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Groupe Régulation Spatiale des Génomes, Département Génomes et GénétiqueInstitut PasteurParis Cedex 15France
  2. 2.CNRS, UMR 3525Paris Cedex 15France
  3. 3.Centre de Bioinformatique, Biostatistique et Biologie IntégrativeUSR 3756, Institut PasteurParis Cedex 15France

Personalised recommendations