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Direct interaction of NRSF with TBP: chromatin reorganization and core promoter repression for neuron-specific gene transcription

Nucleic Acids Research
Oxford University Press
Publication Date
DOI: 10.1093/nar/gkh550
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OP-NARE131294 1..16 Dissecting the chromatin interactome of microRNA genes Dijun Chen1,2,3, Liang-Yu Fu2, Zhao Zhang1, Guoliang Li2,4, Hang Zhang1, Li Jiang1, Andrew P. Harrison5, Hugh P. Shanahan6, Christian Klukas3, Hong-Yu Zhang2, Yijun Ruan2,4,*, Ling-Ling Chen2,* and Ming Chen1,* 1Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China, 2Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China, 3Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany, 4The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA, 5Department of Mathematical Sciences and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK and 6Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK Received September 15, 2013; Revised November 18, 2013; Accepted November 20, 2013 ABSTRACT Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the tran- scriptional regulation of MIRs. We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II–associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display wide- spread communication in those transcriptionally active communities. Moreover, miRNA–target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which th

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