Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin

Summary: Context-specific activities of transcription regulators (TRs) in the nucleus modulate spatiotemporal gene expression precisely. Using the largest ChIP-seq data and chromatin loops in the human K562 cell line, we initially interrogated TR cooperation in 3D chromatin via a graphical model and...

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Autores principales:	Xianfu Yi, Zhanye Zheng, Hang Xu, Yao Zhou, Dandan Huang, Jianhua Wang, Xiangling Feng, Ke Zhao, Xutong Fan, Shijie Zhang, Xiaobao Dong, Zhao Wang, Yujun Shen, Hui Cheng, Lei Shi, Mulin Jun Li
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Genetics Molecular genetics Bioinformatics Science Q
Acceso en línea:	https://doaj.org/article/35a57d76d27143a89fd9b8af06327582
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spelling	oai:doaj.org-article:35a57d76d27143a89fd9b8af063275822021-11-28T04:37:01ZInterrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin2589-004210.1016/j.isci.2021.103468https://doaj.org/article/35a57d76d27143a89fd9b8af063275822021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2589004221014395https://doaj.org/toc/2589-0042Summary: Context-specific activities of transcription regulators (TRs) in the nucleus modulate spatiotemporal gene expression precisely. Using the largest ChIP-seq data and chromatin loops in the human K562 cell line, we initially interrogated TR cooperation in 3D chromatin via a graphical model and revealed many known and novel TRs manipulating context-specific pathways. To explore TR cooperation across broad tissue/cell types, we systematically leveraged large-scale open chromatin profiles, computational footprinting, and high-resolution chromatin interactions to investigate tissue/cell type-specific TR cooperation. We first delineated a landscape of TR cooperation across 40 human tissue/cell types. Network modularity analyses uncovered the commonality and specificity of TR cooperation in different conditions. We also demonstrated that TR cooperation information can better interpret the disease-causal variants identified by genome-wide association studies and recapitulate cell states during neural development. Our study characterizes shared and unique patterns of TR cooperation associated with the cell type specificity of gene regulation in 3D chromatin.Xianfu YiZhanye ZhengHang XuYao ZhouDandan HuangJianhua WangXiangling FengKe ZhaoXutong FanShijie ZhangXiaobao DongZhao WangYujun ShenHui ChengLei ShiMulin Jun LiElsevierarticleGeneticsMolecular geneticsBioinformaticsScienceQENiScience, Vol 24, Iss 12, Pp 103468- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics Molecular genetics Bioinformatics Science Q
spellingShingle	Genetics Molecular genetics Bioinformatics Science Q Xianfu Yi Zhanye Zheng Hang Xu Yao Zhou Dandan Huang Jianhua Wang Xiangling Feng Ke Zhao Xutong Fan Shijie Zhang Xiaobao Dong Zhao Wang Yujun Shen Hui Cheng Lei Shi Mulin Jun Li Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
description	Summary: Context-specific activities of transcription regulators (TRs) in the nucleus modulate spatiotemporal gene expression precisely. Using the largest ChIP-seq data and chromatin loops in the human K562 cell line, we initially interrogated TR cooperation in 3D chromatin via a graphical model and revealed many known and novel TRs manipulating context-specific pathways. To explore TR cooperation across broad tissue/cell types, we systematically leveraged large-scale open chromatin profiles, computational footprinting, and high-resolution chromatin interactions to investigate tissue/cell type-specific TR cooperation. We first delineated a landscape of TR cooperation across 40 human tissue/cell types. Network modularity analyses uncovered the commonality and specificity of TR cooperation in different conditions. We also demonstrated that TR cooperation information can better interpret the disease-causal variants identified by genome-wide association studies and recapitulate cell states during neural development. Our study characterizes shared and unique patterns of TR cooperation associated with the cell type specificity of gene regulation in 3D chromatin.
format	article
author	Xianfu Yi Zhanye Zheng Hang Xu Yao Zhou Dandan Huang Jianhua Wang Xiangling Feng Ke Zhao Xutong Fan Shijie Zhang Xiaobao Dong Zhao Wang Yujun Shen Hui Cheng Lei Shi Mulin Jun Li
author_facet	Xianfu Yi Zhanye Zheng Hang Xu Yao Zhou Dandan Huang Jianhua Wang Xiangling Feng Ke Zhao Xutong Fan Shijie Zhang Xiaobao Dong Zhao Wang Yujun Shen Hui Cheng Lei Shi Mulin Jun Li
author_sort	Xianfu Yi
title	Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
title_short	Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
title_full	Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
title_fullStr	Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
title_full_unstemmed	Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
title_sort	interrogating cell type-specific cooperation of transcriptional regulators in 3d chromatin
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/35a57d76d27143a89fd9b8af06327582
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Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin

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