MCM complexes are barriers that restrict cohesin-mediated loop extrusion
<jats:title>Abstract</jats:title><jats:p>Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)<jats:sup>1–3</jats:sup>, which contribute to transcription, recombination and genomic stability<jats:sup>4,5</jats:sup>. Cohesin...
| Main Authors: | , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer Science and Business Media LLC
2023
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| Online Access: | https://hdl.handle.net/1721.1/150493 |
| _version_ | 1826207710570348544 |
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| author | Dequeker, Bart JH Scherr, Matthias J Brandão, Hugo B Gassler, Johanna Powell, Sean Gaspar, Imre Flyamer, Ilya M Lalic, Aleksandar Tang, Wen Stocsits, Roman Davidson, Iain F Peters, Jan-Michael Duderstadt, Karl E Mirny, Leonid A Tachibana, Kikuë |
| author2 | Harvard-MIT Program in Health Sciences and Technology |
| author_facet | Harvard-MIT Program in Health Sciences and Technology Dequeker, Bart JH Scherr, Matthias J Brandão, Hugo B Gassler, Johanna Powell, Sean Gaspar, Imre Flyamer, Ilya M Lalic, Aleksandar Tang, Wen Stocsits, Roman Davidson, Iain F Peters, Jan-Michael Duderstadt, Karl E Mirny, Leonid A Tachibana, Kikuë |
| author_sort | Dequeker, Bart JH |
| collection | MIT |
| description | <jats:title>Abstract</jats:title><jats:p>Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)<jats:sup>1–3</jats:sup>, which contribute to transcription, recombination and genomic stability<jats:sup>4,5</jats:sup>. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered<jats:sup>6–12</jats:sup>. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are ‘active’ barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.</jats:p> |
| first_indexed | 2024-09-23T13:53:46Z |
| format | Article |
| id | mit-1721.1/150493 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T13:53:46Z |
| publishDate | 2023 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1504932023-04-13T03:23:19Z MCM complexes are barriers that restrict cohesin-mediated loop extrusion Dequeker, Bart JH Scherr, Matthias J Brandão, Hugo B Gassler, Johanna Powell, Sean Gaspar, Imre Flyamer, Ilya M Lalic, Aleksandar Tang, Wen Stocsits, Roman Davidson, Iain F Peters, Jan-Michael Duderstadt, Karl E Mirny, Leonid A Tachibana, Kikuë Harvard-MIT Program in Health Sciences and Technology <jats:title>Abstract</jats:title><jats:p>Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)<jats:sup>1–3</jats:sup>, which contribute to transcription, recombination and genomic stability<jats:sup>4,5</jats:sup>. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered<jats:sup>6–12</jats:sup>. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are ‘active’ barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.</jats:p> 2023-04-12T18:22:38Z 2023-04-12T18:22:38Z 2022 2023-04-12T18:19:33Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/150493 Dequeker, Bart JH, Scherr, Matthias J, Brandão, Hugo B, Gassler, Johanna, Powell, Sean et al. 2022. "MCM complexes are barriers that restrict cohesin-mediated loop extrusion." Nature, 606 (7912). en 10.1038/S41586-022-04730-0 Nature Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | Dequeker, Bart JH Scherr, Matthias J Brandão, Hugo B Gassler, Johanna Powell, Sean Gaspar, Imre Flyamer, Ilya M Lalic, Aleksandar Tang, Wen Stocsits, Roman Davidson, Iain F Peters, Jan-Michael Duderstadt, Karl E Mirny, Leonid A Tachibana, Kikuë MCM complexes are barriers that restrict cohesin-mediated loop extrusion |
| title | MCM complexes are barriers that restrict cohesin-mediated loop extrusion |
| title_full | MCM complexes are barriers that restrict cohesin-mediated loop extrusion |
| title_fullStr | MCM complexes are barriers that restrict cohesin-mediated loop extrusion |
| title_full_unstemmed | MCM complexes are barriers that restrict cohesin-mediated loop extrusion |
| title_short | MCM complexes are barriers that restrict cohesin-mediated loop extrusion |
| title_sort | mcm complexes are barriers that restrict cohesin mediated loop extrusion |
| url | https://hdl.handle.net/1721.1/150493 |
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