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Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging

Little is known about three-dimensional (3D) genome organization in skeletal muscle stem cells [also called satellite cells (SCs)]. Here, we comprehensively map the 3D genome topology reorganization during mouse SC lineage progression. Specifically, rewiring at the compartment level is most pronounc...

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Autores principales: Zhao, Yu, Ding, Yingzhe, He, Liangqiang, Zhou, Qin, Chen, Xiaona, Li, Yuying, Alfonsi, Maria Vittoria, Wu, Zhenguo, Sun, Hao, Wang, Huating
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9937580/
https://www.ncbi.nlm.nih.gov/pubmed/36800432
http://dx.doi.org/10.1126/sciadv.abo1360
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author Zhao, Yu
Ding, Yingzhe
He, Liangqiang
Zhou, Qin
Chen, Xiaona
Li, Yuying
Alfonsi, Maria Vittoria
Wu, Zhenguo
Sun, Hao
Wang, Huating
author_facet Zhao, Yu
Ding, Yingzhe
He, Liangqiang
Zhou, Qin
Chen, Xiaona
Li, Yuying
Alfonsi, Maria Vittoria
Wu, Zhenguo
Sun, Hao
Wang, Huating
author_sort Zhao, Yu
collection PubMed
description Little is known about three-dimensional (3D) genome organization in skeletal muscle stem cells [also called satellite cells (SCs)]. Here, we comprehensively map the 3D genome topology reorganization during mouse SC lineage progression. Specifically, rewiring at the compartment level is most pronounced when SCs become activated. Marked loss in topologically associating domain (TAD) border insulation and chromatin looping also occurs during early activation process. Meanwhile, TADs can form TAD clusters and super-enhancer–containing TAD clusters orchestrate stage-specific gene expression. Furthermore, we uncover that transcription factor PAX7 is pivotal in enhancer-promoter (E-P) loop formation. We also identify cis-regulatory elements that are crucial for local chromatin organization at Pax7 locus and Pax7 expression. Lastly, we unveil that geriatric SC displays a prominent gain in long-range contacts and loss of TAD border insulation. Together, our results uncover that 3D chromatin extensively reorganizes at multiple architectural levels and underpins the transcriptome remodeling during SC lineage development and SC aging.
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spelling pubmed-99375802023-02-18 Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging Zhao, Yu Ding, Yingzhe He, Liangqiang Zhou, Qin Chen, Xiaona Li, Yuying Alfonsi, Maria Vittoria Wu, Zhenguo Sun, Hao Wang, Huating Sci Adv Biomedicine and Life Sciences Little is known about three-dimensional (3D) genome organization in skeletal muscle stem cells [also called satellite cells (SCs)]. Here, we comprehensively map the 3D genome topology reorganization during mouse SC lineage progression. Specifically, rewiring at the compartment level is most pronounced when SCs become activated. Marked loss in topologically associating domain (TAD) border insulation and chromatin looping also occurs during early activation process. Meanwhile, TADs can form TAD clusters and super-enhancer–containing TAD clusters orchestrate stage-specific gene expression. Furthermore, we uncover that transcription factor PAX7 is pivotal in enhancer-promoter (E-P) loop formation. We also identify cis-regulatory elements that are crucial for local chromatin organization at Pax7 locus and Pax7 expression. Lastly, we unveil that geriatric SC displays a prominent gain in long-range contacts and loss of TAD border insulation. Together, our results uncover that 3D chromatin extensively reorganizes at multiple architectural levels and underpins the transcriptome remodeling during SC lineage development and SC aging. American Association for the Advancement of Science 2023-02-17 /pmc/articles/PMC9937580/ /pubmed/36800432 http://dx.doi.org/10.1126/sciadv.abo1360 Text en Copyright © 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (https://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
spellingShingle Biomedicine and Life Sciences
Zhao, Yu
Ding, Yingzhe
He, Liangqiang
Zhou, Qin
Chen, Xiaona
Li, Yuying
Alfonsi, Maria Vittoria
Wu, Zhenguo
Sun, Hao
Wang, Huating
Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
title Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
title_full Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
title_fullStr Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
title_full_unstemmed Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
title_short Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
title_sort multiscale 3d genome reorganization during skeletal muscle stem cell lineage progression and aging
topic Biomedicine and Life Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9937580/
https://www.ncbi.nlm.nih.gov/pubmed/36800432
http://dx.doi.org/10.1126/sciadv.abo1360
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