TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples. TADsplimer recaptures splits and mergers of TADs with high accuracy in simulation analyses and defines hundreds of TAD splits...

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Autores principales: Wang, Guangyu, Meng, Qingshu, Xia, Bo, Zhang, Shuo, Lv, Jie, Zhao, Dongyu, Li, Yanqiang, Wang, Xin, Zhang, Lili, Cooke, John P., Cao, Qi, Chen, Kaifu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114812/
https://www.ncbi.nlm.nih.gov/pubmed/32241291
http://dx.doi.org/10.1186/s13059-020-01992-7
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author Wang, Guangyu
Meng, Qingshu
Xia, Bo
Zhang, Shuo
Lv, Jie
Zhao, Dongyu
Li, Yanqiang
Wang, Xin
Zhang, Lili
Cooke, John P.
Cao, Qi
Chen, Kaifu
author_facet Wang, Guangyu
Meng, Qingshu
Xia, Bo
Zhang, Shuo
Lv, Jie
Zhao, Dongyu
Li, Yanqiang
Wang, Xin
Zhang, Lili
Cooke, John P.
Cao, Qi
Chen, Kaifu
author_sort Wang, Guangyu
collection PubMed
description We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples. TADsplimer recaptures splits and mergers of TADs with high accuracy in simulation analyses and defines hundreds of TAD splits and mergers between pairs of different cell types, such as endothelial cells and fibroblasts. Our work reveals a key role for TAD remodeling in epigenetic regulation of transcription and delivers the first tool for the community to perform dynamic analysis of TAD splits and mergers in numerous biological and disease models.
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spelling pubmed-71148122020-04-07 TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription Wang, Guangyu Meng, Qingshu Xia, Bo Zhang, Shuo Lv, Jie Zhao, Dongyu Li, Yanqiang Wang, Xin Zhang, Lili Cooke, John P. Cao, Qi Chen, Kaifu Genome Biol Method We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples. TADsplimer recaptures splits and mergers of TADs with high accuracy in simulation analyses and defines hundreds of TAD splits and mergers between pairs of different cell types, such as endothelial cells and fibroblasts. Our work reveals a key role for TAD remodeling in epigenetic regulation of transcription and delivers the first tool for the community to perform dynamic analysis of TAD splits and mergers in numerous biological and disease models. BioMed Central 2020-04-02 /pmc/articles/PMC7114812/ /pubmed/32241291 http://dx.doi.org/10.1186/s13059-020-01992-7 Text en © The Author(s) 2020 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Wang, Guangyu
Meng, Qingshu
Xia, Bo
Zhang, Shuo
Lv, Jie
Zhao, Dongyu
Li, Yanqiang
Wang, Xin
Zhang, Lili
Cooke, John P.
Cao, Qi
Chen, Kaifu
TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
title TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
title_full TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
title_fullStr TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
title_full_unstemmed TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
title_short TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
title_sort tadsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114812/
https://www.ncbi.nlm.nih.gov/pubmed/32241291
http://dx.doi.org/10.1186/s13059-020-01992-7
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