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Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells

The three-dimensional configuration of the genome ensures cell type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we used in situ high-throughput chromosome conformation (in situ Hi-C), RNA sequencing (RNA-seq) and chromatin immunoprecip...

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Autores principales: Tian, Geng G., Zhao, Xinyan, Hou, Changliang, Xie, Wenhai, Li, Xiaoyong, Wang, Yinjuan, Wang, Lijuan, Li, Hua, Zhao, Xiaodong, Li, Jing, Wu, Ji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8724064/
https://www.ncbi.nlm.nih.gov/pubmed/34981210
http://dx.doi.org/10.1007/s00018-021-04107-y
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author Tian, Geng G.
Zhao, Xinyan
Hou, Changliang
Xie, Wenhai
Li, Xiaoyong
Wang, Yinjuan
Wang, Lijuan
Li, Hua
Zhao, Xiaodong
Li, Jing
Wu, Ji
author_facet Tian, Geng G.
Zhao, Xinyan
Hou, Changliang
Xie, Wenhai
Li, Xiaoyong
Wang, Yinjuan
Wang, Lijuan
Li, Hua
Zhao, Xiaodong
Li, Jing
Wu, Ji
author_sort Tian, Geng G.
collection PubMed
description The three-dimensional configuration of the genome ensures cell type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we used in situ high-throughput chromosome conformation (in situ Hi-C), RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to characterize the high-order chromatin structure signature of female germline stem cells (FGSCs) and identify its regulating key factor based on the data-driven of multiple omics data. By comparison with pluripotent stem cells (PSCs), adult stem cells (ASCs), and somatic cells at three major levels of chromatin architecture, A/B compartments, topologically associating domains, and chromatin loops, the chromatin architecture of FGSCs was most similar to that of other ASCs and largely different from that of PSCs and somatic cells. After integrative analysis of the three-dimensional chromatin structure, active compartment-associating loops (aCALs) were identified as a signature of high-order chromatin organization in FGSCs, which revealed that CCCTC-binding factor was a major factor to maintain the properties of FGSCs through regulation of aCALs. We found FGSCs belong to ASCs at chromatin structure level and characterized aCALs as the high-order chromatin structure signature of FGSCs. Furthermore, CTCF was identified to play a key role in regulating aCALS to maintain the biological functions of FGSCs. These data provide a valuable resource for future studies of the features of chromatin organization in mammalian stem cells and further understanding of the fundamental characteristics of FGSCs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-021-04107-y.
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spelling pubmed-87240642022-01-13 Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells Tian, Geng G. Zhao, Xinyan Hou, Changliang Xie, Wenhai Li, Xiaoyong Wang, Yinjuan Wang, Lijuan Li, Hua Zhao, Xiaodong Li, Jing Wu, Ji Cell Mol Life Sci Original Article The three-dimensional configuration of the genome ensures cell type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we used in situ high-throughput chromosome conformation (in situ Hi-C), RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to characterize the high-order chromatin structure signature of female germline stem cells (FGSCs) and identify its regulating key factor based on the data-driven of multiple omics data. By comparison with pluripotent stem cells (PSCs), adult stem cells (ASCs), and somatic cells at three major levels of chromatin architecture, A/B compartments, topologically associating domains, and chromatin loops, the chromatin architecture of FGSCs was most similar to that of other ASCs and largely different from that of PSCs and somatic cells. After integrative analysis of the three-dimensional chromatin structure, active compartment-associating loops (aCALs) were identified as a signature of high-order chromatin organization in FGSCs, which revealed that CCCTC-binding factor was a major factor to maintain the properties of FGSCs through regulation of aCALs. We found FGSCs belong to ASCs at chromatin structure level and characterized aCALs as the high-order chromatin structure signature of FGSCs. Furthermore, CTCF was identified to play a key role in regulating aCALS to maintain the biological functions of FGSCs. These data provide a valuable resource for future studies of the features of chromatin organization in mammalian stem cells and further understanding of the fundamental characteristics of FGSCs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-021-04107-y. Springer International Publishing 2022-01-03 2022 /pmc/articles/PMC8724064/ /pubmed/34981210 http://dx.doi.org/10.1007/s00018-021-04107-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Original Article
Tian, Geng G.
Zhao, Xinyan
Hou, Changliang
Xie, Wenhai
Li, Xiaoyong
Wang, Yinjuan
Wang, Lijuan
Li, Hua
Zhao, Xiaodong
Li, Jing
Wu, Ji
Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells
title Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells
title_full Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells
title_fullStr Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells
title_full_unstemmed Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells
title_short Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells
title_sort integrative analysis of the 3d genome structure reveals that ctcf maintains the properties of mouse female germline stem cells
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8724064/
https://www.ncbi.nlm.nih.gov/pubmed/34981210
http://dx.doi.org/10.1007/s00018-021-04107-y
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