KMS Of Academy of mathematics and systems sciences, CAS
Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data | |
Wang, Yong1,2; Jiang, Rui1,3,4; Wong, Wing Hung1 | |
2016-06-01 | |
发表期刊 | NATIONAL SCIENCE REVIEW |
ISSN | 2095-5138 |
卷号 | 3期号:2页码:240-251 |
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. |
关键词 | gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration |
DOI | 10.1093/nsr/nww025 |
语种 | 英语 |
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 |
WOS类目 | Multidisciplinary Sciences |
WOS记录号 | WOS:000379759700025 |
出版者 | OXFORD UNIV PRESS |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://ir.amss.ac.cn/handle/2S8OKBNM/23166 |
专题 | 应用数学研究所 |
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. |
条目包含的文件 | 条目无相关文件。 |
除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。
修改评论