Systematic evaluation of chromosome conformation capture assays
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 experimenta...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer Science and Business Media LLC
2021
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| Online Access: | https://hdl.handle.net/1721.1/138405 |
| _version_ | 1811074931051462656 |
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| author | Akgol Oksuz, Betul Yang, Liyan Abraham, Sameer Venev, Sergey V Krietenstein, Nils Parsi, Krishna Mohan Ozadam, Hakan Oomen, Marlies E Nand, Ankita Mao, Hui Genga, Ryan MJ Maehr, Rene Rando, Oliver J Mirny, Leonid A Gibcus, Johan H Dekker, Job |
| author2 | Massachusetts Institute of Technology. Department of Physics |
| author_facet | Massachusetts Institute of Technology. Department of Physics Akgol Oksuz, Betul Yang, Liyan Abraham, Sameer Venev, Sergey V Krietenstein, Nils Parsi, Krishna Mohan Ozadam, Hakan Oomen, Marlies E Nand, Ankita Mao, Hui Genga, Ryan MJ Maehr, Rene Rando, Oliver J Mirny, Leonid A Gibcus, Johan H Dekker, Job |
| author_sort | Akgol Oksuz, Betul |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T09:57:31Z |
| format | Article |
| id | mit-1721.1/138405 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T09:57:31Z |
| publishDate | 2021 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1384052024-03-19T17:28:19Z Systematic evaluation of chromosome conformation capture assays Akgol Oksuz, Betul Yang, Liyan Abraham, Sameer Venev, Sergey V Krietenstein, Nils Parsi, Krishna Mohan Ozadam, Hakan Oomen, Marlies E Nand, Ankita Mao, Hui Genga, Ryan MJ Maehr, Rene Rando, Oliver J Mirny, Leonid A Gibcus, Johan H Dekker, Job Massachusetts Institute of Technology. Department of Physics Massachusetts Institute of Technology. Institute for Medical Engineering & Science 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. 2021-12-09T14:03:51Z 2021-12-09T14:03:51Z 2021-09 2021-12-09T13:55:20Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/138405 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). en 10.1038/s41592-021-01248-7 Nature Methods Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | Akgol Oksuz, Betul Yang, Liyan Abraham, Sameer Venev, Sergey V Krietenstein, Nils Parsi, Krishna Mohan Ozadam, Hakan Oomen, Marlies E Nand, Ankita Mao, Hui Genga, Ryan MJ Maehr, Rene Rando, Oliver J Mirny, Leonid A Gibcus, Johan H Dekker, Job Systematic evaluation of chromosome conformation capture assays |
| title | Systematic evaluation of chromosome conformation capture assays |
| title_full | Systematic evaluation of chromosome conformation capture assays |
| title_fullStr | Systematic evaluation of chromosome conformation capture assays |
| title_full_unstemmed | Systematic evaluation of chromosome conformation capture assays |
| title_short | Systematic evaluation of chromosome conformation capture assays |
| title_sort | systematic evaluation of chromosome conformation capture assays |
| url | https://hdl.handle.net/1721.1/138405 |
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