Chromosome organization by one-sided and two-sided loop extrusion
© 2020, eLife Sciences Publications Ltd. All rights reserved. SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop ext...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications, Ltd
2021
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| Online Access: | https://hdl.handle.net/1721.1/138400 |
| _version_ | 1826198873239977984 |
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| author | Banigan, Edward J van den Berg, Aafke A Brandão, Hugo B Marko, John F Mirny, Leonid A |
| author_facet | Banigan, Edward J van den Berg, Aafke A Brandão, Hugo B Marko, John F Mirny, Leonid A |
| author_sort | Banigan, Edward J |
| collection | MIT |
| description | © 2020, eLife Sciences Publications Ltd. All rights reserved. SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a “one-sided” manner. We therefore simulate one-sided loop extrusion to investigate whether “one-sided” complexes can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by “two-sided” loop extruders. While one-sided loop extrusion cannot reproduce these phenomena, variants can recapitulate in vivo observations. We predict that SMC complexes in vivo constitute effectively two-sided motors or exhibit biased loading and propose relevant experiments. Our work suggests that loop extrusion is a viable general mechanism of chromatin organization. |
| first_indexed | 2024-09-23T11:11:01Z |
| format | Article |
| id | mit-1721.1/138400 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T11:11:01Z |
| publishDate | 2021 |
| publisher | eLife Sciences Publications, Ltd |
| record_format | dspace |
| spelling | mit-1721.1/1384002021-12-10T03:24:45Z Chromosome organization by one-sided and two-sided loop extrusion Banigan, Edward J van den Berg, Aafke A Brandão, Hugo B Marko, John F Mirny, Leonid A © 2020, eLife Sciences Publications Ltd. All rights reserved. SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a “one-sided” manner. We therefore simulate one-sided loop extrusion to investigate whether “one-sided” complexes can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by “two-sided” loop extruders. While one-sided loop extrusion cannot reproduce these phenomena, variants can recapitulate in vivo observations. We predict that SMC complexes in vivo constitute effectively two-sided motors or exhibit biased loading and propose relevant experiments. Our work suggests that loop extrusion is a viable general mechanism of chromatin organization. 2021-12-09T13:04:53Z 2021-12-09T13:04:53Z 2020 2021-12-09T12:59:16Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/138400 Banigan, Edward J, van den Berg, Aafke A, Brandão, Hugo B, Marko, John F and Mirny, Leonid A. 2020. "Chromosome organization by one-sided and two-sided loop extrusion." eLife, 9. en 10.7554/ELIFE.53558 eLife Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf eLife Sciences Publications, Ltd eLife |
| spellingShingle | Banigan, Edward J van den Berg, Aafke A Brandão, Hugo B Marko, John F Mirny, Leonid A Chromosome organization by one-sided and two-sided loop extrusion |
| title | Chromosome organization by one-sided and two-sided loop extrusion |
| title_full | Chromosome organization by one-sided and two-sided loop extrusion |
| title_fullStr | Chromosome organization by one-sided and two-sided loop extrusion |
| title_full_unstemmed | Chromosome organization by one-sided and two-sided loop extrusion |
| title_short | Chromosome organization by one-sided and two-sided loop extrusion |
| title_sort | chromosome organization by one sided and two sided loop extrusion |
| url | https://hdl.handle.net/1721.1/138400 |
| work_keys_str_mv | AT baniganedwardj chromosomeorganizationbyonesidedandtwosidedloopextrusion AT vandenbergaafkea chromosomeorganizationbyonesidedandtwosidedloopextrusion AT brandaohugob chromosomeorganizationbyonesidedandtwosidedloopextrusion AT markojohnf chromosomeorganizationbyonesidedandtwosidedloopextrusion AT mirnyleonida chromosomeorganizationbyonesidedandtwosidedloopextrusion |