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Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization
Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes. Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapid...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202648/ https://www.ncbi.nlm.nih.gov/pubmed/37223244 http://dx.doi.org/10.1093/nsr/nwad073 |
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author | Zhou, Sijie Wu, Yi Zhao, Yu Zhang, Zhen Jiang, Limin Liu, Lin Zhang, Yan Tang, Jijun Yuan, Ying-Jin |
author_facet | Zhou, Sijie Wu, Yi Zhao, Yu Zhang, Zhen Jiang, Limin Liu, Lin Zhang, Yan Tang, Jijun Yuan, Ying-Jin |
author_sort | Zhou, Sijie |
collection | PubMed |
description | Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes. Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural variations. Here, we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes (synII, synIII, synV, circular synVI, synIXR and synX). Remarkably, we find that the rearrangement events exhibit a specific landscape of frequency. We further reveal that the landscape is shaped by the combined effects of chromatin accessibility and spatial contact probability. The rearrangements tend to occur in 3D spatially proximal and chromatin-accessible regions. The enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution, and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution. |
format | Online Article Text |
id | pubmed-10202648 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-102026482023-05-23 Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization Zhou, Sijie Wu, Yi Zhao, Yu Zhang, Zhen Jiang, Limin Liu, Lin Zhang, Yan Tang, Jijun Yuan, Ying-Jin Natl Sci Rev Research Article Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes. Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural variations. Here, we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes (synII, synIII, synV, circular synVI, synIXR and synX). Remarkably, we find that the rearrangement events exhibit a specific landscape of frequency. We further reveal that the landscape is shaped by the combined effects of chromatin accessibility and spatial contact probability. The rearrangements tend to occur in 3D spatially proximal and chromatin-accessible regions. The enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution, and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution. Oxford University Press 2023-03-17 /pmc/articles/PMC10202648/ /pubmed/37223244 http://dx.doi.org/10.1093/nsr/nwad073 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Zhou, Sijie Wu, Yi Zhao, Yu Zhang, Zhen Jiang, Limin Liu, Lin Zhang, Yan Tang, Jijun Yuan, Ying-Jin Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization |
title | Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization |
title_full | Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization |
title_fullStr | Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization |
title_full_unstemmed | Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization |
title_short | Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization |
title_sort | dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202648/ https://www.ncbi.nlm.nih.gov/pubmed/37223244 http://dx.doi.org/10.1093/nsr/nwad073 |
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