Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

doi:10.1093/nsr/nww025

	Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data
	Wang, Yong 1,2; Jiang, Rui 1,3,4; Wong, Wing Hung 1
刊名	NATIONAL SCIENCE REVIEW
	2016-06-01
卷号	3 期号:2 页码:240-251
关键词	gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration
ISSN号	2095-5138
DOI	10.1093/nsr/nww025
英文摘要	Cell packs a lot of genetic and regulatory information through a structure known as chromatin, i.e. DNA is wrapped around histone proteins and is tightly packed in a remarkable way. To express a gene in a specific coding region, the chromatin would open up and DNA loop may be formed by interacting enhancers and promoters. Furthermore, the mediator and cohesion complexes, sequence-specific transcription factors, and RNA polymerase II are recruited and work together to elaborately regulate the expression level. It is in pressing need to understand how the information, about when, where, and to what degree genes should be expressed, is embedded into chromatin structure and gene regulatory elements. Thanks to large consortia such as Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenomic projects, extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell types. This rich data offer an exciting opportunity to model the causal regulatory relationship. Here, we will review the current experimental approaches, foundational data, computational problems, interpretive frameworks, and integrative models that will enable the accurate interpretation of regulatory landscape. Particularly, we will discuss the efforts to organize, analyze, model, and integrate the DNA accessibility data, transcriptional data, and functional genomic regions together. We believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.
资助项目	NIH[P50HG007735] ; NIH[R01HG007834] ; Chinese Academy of Sciences ; Tsinghua University ; NSFC[11422108] ; NSFC[61573207]
WOS研究方向	Science & Technology - Other Topics
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000379759700025
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/23165]
专题	中国科学院数学与系统科学研究院
通讯作者	Wong, Wing Hung
作者单位	1.Stanford Univ, Dept Stat, Dept Biomed Data Sci, BioX Program, Stanford, CA 94305 USA 2.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100080, Peoples R China 3.Tsinghua Univ, MOE Key Lab Bioinformat, Bioinformat Div, Dept Automat, Beijing 100084, Peoples R China 4.Tsinghua Univ, Ctr Synthet & Syst Biol, TNLIST, Dept Automat, Beijing 100084, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yong,Jiang, Rui,Wong, Wing Hung. Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data[J]. NATIONAL SCIENCE REVIEW,2016,3(2):240-251.
APA	Wang, Yong,Jiang, Rui,&Wong, Wing Hung.(2016).Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data.NATIONAL SCIENCE REVIEW,3(2),240-251.
MLA	Wang, Yong,et al."Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data".NATIONAL SCIENCE REVIEW 3.2(2016):240-251.