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Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Li, Guoliang and Fisher-Aylor, Katherine I. and Mortazavi, Ali and Wold, Barbara (2012) Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell, 148 (1-2). pp. 84-98. ISSN 0092-8674. PMCID PMC3339270. doi:10.1016/j.cell.2011.12.014. https://resolver.caltech.edu/CaltechAUTHORS:20120224-130228176

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Abstract

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIAPET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1016/j.cell.2011.12.014DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339270/PubMed CentralArticle
ORCID:
AuthorORCID
Li, Guoliang0000-0003-0063-1585
Mortazavi, Ali0000-0002-4259-6362
Wold, Barbara0000-0003-3235-8130
Additional Information:© 2012 Elsevier Inc. Received 18 July 2011. Revised 21 October 2011. Accepted 12 December 2011. Available online 19 January 2012. Published: January 19, 2012. We acknowledge the Genome Technology and Biology Group at the Genome Institute of Singapore for technical support. This work was supported by Singapore A*STAR and an NIH grant (HG004456) to Y.R.
Funders:
Funding AgencyGrant Number
Agency for Science, Technology and Research (A*STAR)UNSPECIFIED
NIHHG004456
Issue or Number:1-2
PubMed Central ID:PMC3339270
DOI:10.1016/j.cell.2011.12.014
Record Number:CaltechAUTHORS:20120224-130228176
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20120224-130228176
Official Citation:Guoliang Li, Xiaoan Ruan, Raymond K. Auerbach, Kuljeet Singh Sandhu, Meizhen Zheng, Ping Wang, Huay Mei Poh, Yufen Goh, Joanne Lim, Jingyao Zhang, Hui Shan Sim, Su Qin Peh, Fabianus Hendriyan Mulawadi, Chin Thing Ong, Yuriy L. Orlov, Shuzhen Hong, Zhizhuo Zhang, Steve Landt, Debasish Raha, Ghia Euskirchen, Chia-Lin Wei, Weihong Ge, Huaien Wang, Carrie Davis, Katherine I. Fisher-Aylor, Ali Mortazavi, Mark Gerstein, Thomas Gingeras, Barbara Wold, Yi Sun, Melissa J. Fullwood, Edwin Cheung, Edison Liu, Wing-Kin Sung, Michael Snyder, Yijun Ruan, Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation, Cell, Volume 148, Issues 1–2, 20 January 2012, Pages 84-98, ISSN 0092-8674, 10.1016/j.cell.2011.12.014. (http://www.sciencedirect.com/science/article/pii/S0092867411015170)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:29462
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:24 Feb 2012 21:44
Last Modified:09 Nov 2021 17:07

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