Systematic evaluation of chromosome conformation capture assays
Research output: Contribution to journal › Journal article › Research › peer-review
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.
Original language | English |
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Journal | Nature Methods |
Volume | 18 |
Issue number | 9 |
Pages (from-to) | 1046-1055 |
Number of pages | 10 |
ISSN | 1548-7091 |
DOIs | |
Publication status | Published - Sep 2021 |
Externally published | Yes |
Bibliographical note
© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.
- Cell Line, Chromatin/chemistry, Chromosomes, Human/chemistry, Cross-Linking Reagents/chemistry, Databases, Factual, Genetic Techniques, Human Embryonic Stem Cells/cytology, Humans
Research areas
ID: 301924683