KMS Of Academy of mathematics and systems sciences, CAS
| Modeling gene regulation from paired expression and chromatin accessibility data | |
Duren, Zhana1,2,3; Chen, Xi2; Jiang, Rui3,4,5; Wang, Yong1 ; Wong, Wing Hung2
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| 2017-06-20 | |
| Source Publication | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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| ISSN | 0027-8424 |
| Volume | 114Issue:25Pages:E4914-E4923 |
| Abstract | 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. |
| Keyword | gene regulation transcription factor regulatory element chromatin regulator chromatin activity |
| DOI | 10.1073/pnas.1704553114 |
| Language | 英语 |
| Funding Project | 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 Research Area | Science & Technology - Other Topics |
| WOS Subject | Multidisciplinary Sciences |
| WOS ID | WOS:000403687300006 |
| Publisher | NATL ACAD SCIENCES |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/25846 |
| Collection | 应用数学研究所 |
| Corresponding Author | Jiang, Rui; Wang, Yong; Wong, Wing Hung |
| Affiliation | 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 |
| Recommended Citation 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. |
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