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

Guangyu Wang; Qingshu Meng; Bo Xia; Shuo Zhang; Jie Lv; Dongyu Zhao; Yanqiang Li; Xin Wang; Lili Zhang; John P. Cooke; Qi Cao; Kaifu Chen

doi:10.1186/s13059-020-01992-7

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

Guangyu Wang, Qingshu Meng, Bo Xia, Shuo Zhang, Jie Lv, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao, Kaifu Chen

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

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.

Original language	English (US)
Article number	84
Journal	Genome Biology
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s13059-020-01992-7
State	Published - Apr 2 2020

Keywords

Bioinformatics
Chromatin conformation
Computational biology
Epigenomics
Hi-C
Histone modification
Topologically associating domains

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/s13059-020-01992-7

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abstract = "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.",

keywords = "Bioinformatics, Chromatin conformation, Computational biology, Epigenomics, Hi-C, Histone modification, Topologically associating domains",

author = "Guangyu Wang and Qingshu Meng and Bo Xia and Shuo Zhang and Jie Lv and Dongyu Zhao and Yanqiang Li and Xin Wang and Lili Zhang and Cooke, {John P.} and Qi Cao and Kaifu Chen",

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T1 - TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

AU - Wang, Guangyu

AU - Meng, Qingshu

AU - Xia, Bo

AU - Zhang, Shuo

AU - Lv, Jie

AU - Zhao, Dongyu

AU - Li, Yanqiang

AU - Wang, Xin

AU - Zhang, Lili

AU - Cooke, John P.

AU - Cao, Qi

AU - Chen, Kaifu

PY - 2020/4/2

Y1 - 2020/4/2

N2 - 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.

AB - 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.

KW - Bioinformatics

KW - Chromatin conformation

KW - Computational biology

KW - Epigenomics

KW - Hi-C

KW - Histone modification

KW - Topologically associating domains

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

Abstract

Keywords

ASJC Scopus subject areas

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