SMC Complexes pp 105-118 | Cite as

Chromosome Conformation Capture with Deep Sequencing to Study the Roles of the Structural Maintenance of Chromosomes Complex In Vivo

  • Tung B. K. LeEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2004)


Recent applications of chromosome conformation capture with deep sequencing (Hi-C and other C techniques) has enabled high-throughput investigations and driven major advances in understanding chromosome organization in bacteria and eukaryotes. C techniques reveal systematically the identities of interacting DNA and the frequency of each interaction in vivo. Beyond a bird’s-eye view survey of the global chromosome architecture, C techniques together with genetic perturbation have proven to be powerful in understanding factors that shape chromosome architectures. The structural maintenance of chromosomes (SMC) proteins play major roles in organizing the chromosomes from bacteria to humans, and C techniques have contributed to understanding their mechanism and impact on genome organization in a cellular context. Here, I describe a Hi-C protocol, a variant of C techniques, to construct genome-wide DNA contact maps for bacteria. This protocol is optimized for the gram-negative bacterium Caulobacter crescentus, but it can be readily adapted for any bacterial species of interest.

Key words

Chromosome conformation capture Hi-C Deep sequencing Chromosome organization Structural maintenance of chromosomes SMC Caulobacter crescentus 



This research is supported by a Royal Society University Research Fellowship (UF140053 and RG150448) and a BBSRC grant (BB/P018165/1) to T.B.K.L. The Hi-C technique was first optimized for Caulobacter crescentus when the author was a postdoctoral fellow in the lab of Prof. Michael Laub. The author thanks Prof. Michael Laub and Dr. Mark Umbarger for support and advice during the optimization of this protocol.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Molecular MicrobiologyJohn Innes CentreNorwichUK

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