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  Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

Downes, D. J., Smith, A. L., Karpinska, M. A., Velychko, T., Rue-Albrecht, K., Sims, D., et al. (2022). Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature Protocols, 17(2), 445-475. doi:10.1038/s41596-021-00651-w.

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 Creators:
Downes, D. J., Author
Smith, A. L., Author
Karpinska, M. A.1, Author              
Velychko, T.2, Author              
Rue-Albrecht, K., Author
Sims, D., Author
Milne, T. A., Author
Davies, J. O. J., Author
Oudelaar, A. M.1, Author              
Hughes, J. R., Author
Affiliations:
1Lise Meitner Group Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society, ou_3350292              
2Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society, ou_3350224              

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Free keywords: Chromatin analysis; Data processing; Functional genomics; Gene regulation
 Abstract: Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample 3C material, including the Capture-C family of protocols. Capture-C methods use oligonucleotides to enrich for interactions of interest from sequencing-ready 3C libraries. This approach is modular and has been adapted and optimized to work for sampling of disperse DNA elements (NuTi Capture-C), including from low cell inputs (LI Capture-C), as well as to generate Hi-C like maps for specific regions of interest (Tiled-C) and to interrogate multiway interactions (Tri-C). We present the design, experimental protocol and analysis pipeline for NuTi Capture-C in addition to the variations for generation of LI Capture-C, Tiled-C and Tri-C data. The entire procedure can be performed in 3 weeks and requires standard molecular biology skills and equipment, access to a next-generation sequencing platform, and basic bioinformatic skills. Implemented with other sequencing technologies, these methods can be used to identify regulatory interactions and to compare the structural organization of the genome in different cell types and genetic models.

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Language(s): eng - English
 Dates: 2022-02-042022-02-22
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41596-021-00651-w
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Title: Nature Protocols
Source Genre: Journal
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Pages: - Volume / Issue: 17 (2) Sequence Number: - Start / End Page: 445 - 475 Identifier: -