Abstract
The three-dimensional structure of the chromosome is encoded within its sequence and regulates activities such as replication and transcription. This necessitates the study of the spatial organization of the chromosome in relation to the underlying sequence. Chromosome conformation capture (3C) techniques are proximity ligation-based approaches that simplify the three-dimensional architecture of the chromosome into a one-dimensional library of hybrid ligation junctions. Deciphering the information contained in these libraries resolves chromosome architecture in a sequence-specific manner. This chapter describes the preparation of 3C libraries for bacteria and archaea. It details how the three-dimensional architecture of local chromatin can be extracted from the 3C library using qPCR (3C-qPCR), and it summarizes the processing of 3C libraries for next-generation sequencing (3C-Seq) for a study of global chromosome organization.
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Acknowledgments
This work was supported by grants from the Netherlands Organization for Scientific Research [VICI 016.160.613 and OCENW.GROOT.2019.012], the FOM Foundation for Fundamental Research on Matter program ‘Crowd management: The physics of genome processing in complex environments and the Human Frontier Science Program (HFSP) [RGP0014/2014].
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Rashid, FZ.M., Detmar, L., Dame, R.T. (2022). Chromosome Conformation Capture in Bacteria and Archaea. In: Peeters, E., Bervoets, I. (eds) Prokaryotic Gene Regulation. Methods in Molecular Biology, vol 2516. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2413-5_1
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DOI: https://doi.org/10.1007/978-1-0716-2413-5_1
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