Systematic evaluation of chromosome conformation capture assays
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s41592-021-01248-7.pdf
Description
Published version
Size
18.3 MB
Format
Adobe PDF
Checksum (MD5)
58fa7fe06837c0ec77954c3381700a41
Author(s)
Akgol Oksuz, Betul
Yang, Liyan
Abraham, Sameer
Venev, Sergey V
Krietenstein, Nils
Parsi, Krishna Mohan
Ozadam, Hakan
Oomen, Marlies E
Nand, Ankita
Mao, Hui
Date Issued
September 2021
Journal
Nature Methods
Publisher
Springer Science and Business Media LLC
Citation
Akgol Oksuz, Betul, Yang, Liyan, Abraham, Sameer, Venev, Sergey V, Krietenstein, Nils et al. 2021. "Systematic evaluation of chromosome conformation capture assays." Nature Methods, 18 (9).
Version
Final published version
Abstract
Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.
MIT Department
Massachusetts Institute of Technology. Department of Physics
Massachusetts Institute of Technology. Institute for Medical Engineering & Science
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1038/s41592-021-01248-7
