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Modeling gene regulation from paired expression and chromatin accessibility data

文献类型：期刊论文

作者Duren, Zhana1,2,3; Chen, Xi2; Jiang, Rui3,4,5; Wang, Yong1; Wong, Wing Hung2
刊名PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
出版日期2017-06-20
卷号114期号:25页码:E4914-E4923
关键词gene regulation transcription factor regulatory element chromatin regulator chromatin activity
ISSN号0027-8424
DOI10.1073/pnas.1704553114
英文摘要The rapid increase of genome-wide datasets on gene expression, chromatin states, and transcription factor (TF) binding locations offers an exciting opportunity to interpret the information encoded in genomes and epigenomes. This task can be challenging as it requires joint modeling of context-specific activation of cis-regulatory elements (REs) and the effects on transcription of associated regulatory factors. To meet this challenge, we propose a statistical approach based on paired expression and chromatin accessibility (PECA) data across diverse cellular contexts. In our approach, we model (i) the localization to REs of chromatin regulators (CRs) based on their interaction with sequence-specific TFs, (ii) the activation of REs due to CRs that are localized to them, and (iii) the effect of TFs bound to activated REs on the transcription of target genes (TGs). The transcriptional regulatory network inferred by PECA provides a detailed view of how trans-and cis-regulatory elements work together to affect gene expression in a context-specific manner. We illustrate the feasibility of this approach by analyzing paired expression and accessibility data from the mouse Encyclopedia of DNA Elements (ENCODE) and explore various applications of the resulting model.
资助项目Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13000000] ; NIH[R01HG007834] ; NIH[P50HG007735] ; National Natural Science Foundation of China[11422108] ; National Natural Science Foundation of China[61671444] ; National Natural Science Foundation of China[61621003] ; National Natural Science Foundation of China[61573207]
WOS研究方向Science & Technology - Other Topics
语种英语
WOS记录号WOS:000403687300006
出版者NATL ACAD SCIENCES
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/25845]  
专题应用数学研究所
通讯作者Jiang, Rui; Wang, Yong; Wong, Wing Hung
作者单位1.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China
2.Stanford Univ, Dept Stat, BioX Program, Dept Biomed Data Sci, Stanford, CA 94305 USA
3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
4.Tsinghua Univ, Minist Educ, Key Lab Bioinformat, Bioinformat Div, Beijing 100084, Peoples R China
5.Tsinghua Univ, Ctr Synthet & Syst Biol, Tsinghua Natl Lab Informat Sci & Technol, Dept Automat, Beijing 100084, Peoples R China
推荐引用方式
GB/T 7714		 Duren, Zhana,Chen, Xi,Jiang, Rui,et al. Modeling gene regulation from paired expression and chromatin accessibility data[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2017,114(25):E4914-E4923.
APA Duren, Zhana,Chen, Xi,Jiang, Rui,Wang, Yong,&Wong, Wing Hung.(2017).Modeling gene regulation from paired expression and chromatin accessibility data.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,114(25),E4914-E4923.
MLA Duren, Zhana,et al."Modeling gene regulation from paired expression and chromatin accessibility data".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114.25(2017):E4914-E4923.

入库方式： OAI收割

来源：数学与系统科学研究院

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