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Title: Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
Authors: Li, G.
Ruan, X.
Auerbach, R.K.
Sandhu, K.S.
Zheng, M.
Wang, P.
Poh, H.M.
Goh, Y.
Lim, J.
Zhang, J.
Sim, H.S.
Peh, S.Q.
Mulawadi, F.H.
Ong, C.T.
Orlov, Y.L.
Hong, S.
Zhang, Z.
Landt, S.
Raha, D.
Euskirchen, G.
Wei, C.-L.
Ge, W.
Wang, H.
Davis, C.
Fisher-Aylor, K.I.
Mortazavi, A.
Gerstein, M.
Gingeras, T.
Wold, B.
Sun, Y.
Fullwood, M.J.
Cheung, E.
Liu, E.
Sung, W.-K. 
Snyder, M.
Ruan, Y.
Issue Date: 2012
Citation: Li, G., Ruan, X., Auerbach, R.K., Sandhu, K.S., Zheng, M., Wang, P., Poh, H.M., Goh, Y., Lim, J., Zhang, J., Sim, H.S., Peh, S.Q., Mulawadi, F.H., Ong, C.T., Orlov, Y.L., Hong, S., Zhang, Z., Landt, S., Raha, D., Euskirchen, G., Wei, C.-L., Ge, W., Wang, H., Davis, C., Fisher-Aylor, K.I., Mortazavi, A., Gerstein, M., Gingeras, T., Wold, B., Sun, Y., Fullwood, M.J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., Ruan, Y. (2012). Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148 (1-2) : 84-98. ScholarBank@NUS Repository.
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. © 2012 Elsevier Inc.
Source Title: Cell
ISSN: 00928674
DOI: 10.1016/j.cell.2011.12.014
Appears in Collections:Staff Publications

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