Advertisement

Determination of the 3D Genome Organization of Bacteria Using Hi-C

  • Frédéric G. Crémazy
  • Fatema-Zahra M. Rashid
  • James R. Haycocks
  • Lisa E. Lamberte
  • David C. Grainger
  • Remus T. Dame
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1837)

Abstract

The spatial organization of genomes is based on their hierarchical compartmentalization in topological domains. There is growing evidence that bacterial genomes are organized into insulated domains similar to the Topologically Associating Domains (TADs) detected in eukaryotic cells. Chromosome conformation capture (3C) technologies are used to analyze in vivo DNA proximity based on ligation of distal DNA segments crossed-linked by bridging proteins. By combining 3C and high-throughput sequencing, the Hi-C method reveals genome-wide interactions within topological domains and global genome structure as a whole. This chapter provides detailed guidelines for the preparation of Hi-C sequencing libraries for bacteria.

Key words

Hi-C Chromosome Bacterial chromatin 

Notes

Acknowledgments

This work was supported by grants from the Netherlands Organization for Scientific Research [VICI 016.160.613] and the Human Frontier Science Program (HFSP) [RGP0014/2014].

References

  1. 1.
    Denker A, de Laat W (2016) The second decade of 3C technologies: detailed insights into nuclear organization. Genes Dev 30(12):1357–1382. https://doi.org/10.1101/gad.281964.116 CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376–380. https://doi.org/10.1038/nature11082 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7):1665–1680. https://doi.org/10.1016/j.cell.2014.11.021 CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Lieberman-Aiden E, Lieberman-Aiden E, van Berkum NL, van Berkum NL, Williams L, Williams L, Imakaev M, Imakaev M, Ragoczy T, Ragoczy T, Telling A, Telling A, Amit I, Amit I, Lajoie BR, Lajoie BR, Sabo PJ, Sabo PJ, Dorschner MO, Dorschner MO, Sandstrom R, Sandstrom R, Bernstein B, Bernstein B, Bender MA, Groudine M, Groudine M, Gnirke A, Gnirke A, Stamatoyannopoulos J, Stamatoyannopoulos J, Mirny LA, Mirny LA, Lander ES, Lander ES, Dekker J, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293. https://doi.org/10.1126/science.1181369 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Dame RT, Tark-Dame M (2016) Bacterial chromatin: converging views at different scales. Curr Opin Cell Biol 40:60–65. https://doi.org/10.1016/j.ceb.2016.02.015 CrossRefPubMedGoogle Scholar
  6. 6.
    Le TBK, Imakaev MV, Mirny LA, Laub MT (2013) High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342(6159):731–734. https://doi.org/10.1126/science.1242059 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche J-B, Mozziconacci J, Murray H, Koszul R, Nollmann M (2015) Condensin- and replication-mediated bacterial chromosome folding and origin condensation revealed by hi-C and super-resolution imaging. Mol Cell 59(4):588–602. https://doi.org/10.1016/j.molcel.2015.07.020 CrossRefPubMedGoogle Scholar
  8. 8.
    van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES (2010) Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp (39). https://doi.org/10.3791/1869

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Frédéric G. Crémazy
    • 1
  • Fatema-Zahra M. Rashid
    • 1
  • James R. Haycocks
    • 2
  • Lisa E. Lamberte
    • 2
  • David C. Grainger
    • 2
  • Remus T. Dame
    • 3
  1. 1.Leiden Institute of ChemistryLeiden UniversityLeidenThe Netherlands
  2. 2.School of BiosciencesBirmingham UniversityBirminghamUK
  3. 3.Leiden Institute of Chemistry and Centre for Microbial Cell BiologyLeiden UniversityLeidenThe Netherlands

Personalised recommendations