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|Title:||Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation|
|Source:||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. https://doi.org/10.1016/j.cell.2011.12.014|
|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.|
|Appears in Collections:||Staff Publications|
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