The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers

Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD)...

Descripción completa

Detalles Bibliográficos
Autores principales: Du, Guifang, Li, Hao, Ding, Yang, Jiang, Shuai, Hong, Hao, Gan, Jingbo, Wang, Longteng, Yang, Yuanping, Li, Yinyin, Huang, Xin, Sun, Yu, Tao, Huan, Li, Yaru, Xu, Xiang, Zheng, Yang, Wang, Junting, Bai, Xuemei, Xu, Kang, Li, Yaoshen, Jiang, Qi, Li, Cheng, Chen, Hebing, Bo, Xiaochen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2021
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8050718/
https://www.ncbi.nlm.nih.gov/pubmed/33897976
http://dx.doi.org/10.1016/j.csbj.2021.03.018
_version_ 1783679625464905728
author Du, Guifang
Li, Hao
Ding, Yang
Jiang, Shuai
Hong, Hao
Gan, Jingbo
Wang, Longteng
Yang, Yuanping
Li, Yinyin
Huang, Xin
Sun, Yu
Tao, Huan
Li, Yaru
Xu, Xiang
Zheng, Yang
Wang, Junting
Bai, Xuemei
Xu, Kang
Li, Yaoshen
Jiang, Qi
Li, Cheng
Chen, Hebing
Bo, Xiaochen
author_facet Du, Guifang
Li, Hao
Ding, Yang
Jiang, Shuai
Hong, Hao
Gan, Jingbo
Wang, Longteng
Yang, Yuanping
Li, Yinyin
Huang, Xin
Sun, Yu
Tao, Huan
Li, Yaru
Xu, Xiang
Zheng, Yang
Wang, Junting
Bai, Xuemei
Xu, Kang
Li, Yaoshen
Jiang, Qi
Li, Cheng
Chen, Hebing
Bo, Xiaochen
author_sort Du, Guifang
collection PubMed
description Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a “TAD hierarchical score (TH score)” for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. We demonstrated that the TAD nesting levels of genes in a tumor differ from those in normal tissue. Furthermore, the hierarchical TAD level dynamics were related to transcriptional changes in cancer, and some of the genes in which the hierarchical level was altered were significantly related to the prognosis of cancer patients. Overall, the results of this study suggest that the folding dynamics of TADs are closely related to transcriptional abnormalities in cancers, emphasizing that the function of hierarchical chromatin organization goes beyond simple chromatin packaging efficiency.
format Online
Article
Text
id pubmed-8050718
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Research Network of Computational and Structural Biotechnology
record_format MEDLINE/PubMed
spelling pubmed-80507182021-04-23 The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers Du, Guifang Li, Hao Ding, Yang Jiang, Shuai Hong, Hao Gan, Jingbo Wang, Longteng Yang, Yuanping Li, Yinyin Huang, Xin Sun, Yu Tao, Huan Li, Yaru Xu, Xiang Zheng, Yang Wang, Junting Bai, Xuemei Xu, Kang Li, Yaoshen Jiang, Qi Li, Cheng Chen, Hebing Bo, Xiaochen Comput Struct Biotechnol J Research Article Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a “TAD hierarchical score (TH score)” for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. We demonstrated that the TAD nesting levels of genes in a tumor differ from those in normal tissue. Furthermore, the hierarchical TAD level dynamics were related to transcriptional changes in cancer, and some of the genes in which the hierarchical level was altered were significantly related to the prognosis of cancer patients. Overall, the results of this study suggest that the folding dynamics of TADs are closely related to transcriptional abnormalities in cancers, emphasizing that the function of hierarchical chromatin organization goes beyond simple chromatin packaging efficiency. Research Network of Computational and Structural Biotechnology 2021-03-26 /pmc/articles/PMC8050718/ /pubmed/33897976 http://dx.doi.org/10.1016/j.csbj.2021.03.018 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Du, Guifang
Li, Hao
Ding, Yang
Jiang, Shuai
Hong, Hao
Gan, Jingbo
Wang, Longteng
Yang, Yuanping
Li, Yinyin
Huang, Xin
Sun, Yu
Tao, Huan
Li, Yaru
Xu, Xiang
Zheng, Yang
Wang, Junting
Bai, Xuemei
Xu, Kang
Li, Yaoshen
Jiang, Qi
Li, Cheng
Chen, Hebing
Bo, Xiaochen
The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
title The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
title_full The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
title_fullStr The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
title_full_unstemmed The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
title_short The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
title_sort hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8050718/
https://www.ncbi.nlm.nih.gov/pubmed/33897976
http://dx.doi.org/10.1016/j.csbj.2021.03.018
work_keys_str_mv AT duguifang thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT lihao thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT dingyang thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT jiangshuai thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT honghao thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT ganjingbo thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT wanglongteng thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT yangyuanping thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT liyinyin thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT huangxin thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT sunyu thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT taohuan thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT liyaru thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT xuxiang thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT zhengyang thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT wangjunting thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT baixuemei thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT xukang thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT liyaoshen thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT jiangqi thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT licheng thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT chenhebing thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT boxiaochen thehierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT duguifang hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT lihao hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT dingyang hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT jiangshuai hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT honghao hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT ganjingbo hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT wanglongteng hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT yangyuanping hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT liyinyin hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT huangxin hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT sunyu hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT taohuan hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT liyaru hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT xuxiang hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT zhengyang hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT wangjunting hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT baixuemei hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT xukang hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT liyaoshen hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT jiangqi hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT licheng hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT chenhebing hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers
AT boxiaochen hierarchicalfoldingdynamicsoftopologicallyassociatingdomainsarecloselyrelatedtotranscriptionalabnormalitiesincancers

Ejemplares similares