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Title: Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
Authors: Li, Guoliang
Ruan, Xiaoan
Auerbach, Raymond K.
Sandhu, Kuljeet Singh
Zheng, Meizhen
Wang, Ping
Poh, Huay Mei
Goh, Yufen
Lim, Joanne
Zhang, Jingyao
Sim, Hui Shan
Peh, Su Qin
Mulawadi, Fabianus Hendriyan
Ong, Chin Thing
Orlov, Yuriy L.
Hong, Shuzhen
Zhang, Zhizhuo
Landt, Steve
Raha, Debasish
Euskirchen, Ghia
Wei, Chia-Lin
Ge, Weihong
Wang, Huaien
Davis, Carrie
Fisher-Aylor, Katherine I.
Mortazavi, Ali
Gerstein, Mark
Gingeras, Thomas
Wold, Barbara
Sun, Yi
Cheung, Edwin
Liu, Edison
Sung, Wing-Kin
Snyder, Michael
Ruan, Yijun
Fullwood, Melissa Jane
Keywords: DRNTU::Science::Biological sciences
Issue Date: 2012
Source: Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., et al. (2012). Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell, 148(1), 84-98.
Series/Report no.: Cell
Abstract: Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), 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.
ISSN: 0092-8674
DOI: 10.1016/j.cell.2011.12.014
Rights: © 2012 Elsevier Inc.
Fulltext Permission: none
Fulltext Availability: No Fulltext
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