한빛사 논문
Abstract
Samuel Beck1, Bum-Kyu Lee1, Catherine Rhee1, Jawon Song2, Andrew J. Woo3 & Jonghwan Kim1,4,5,*
1 Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA. 2 Texas Advanced Computing Center, The University of Texas at Austin, Austin, Texas 78758, USA. 3 School of Medicine and Pharmacology, Royal Perth Hospital Unit, The University of Western Australia, Perth, WA 6000, Australia. 4 Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA. 5 Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
*Correspondence to: Jonghwan Kim
Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of 4200 large sequencing data sets to elucidate the regulatory logic of global gene expression programs in mouse embryonic stem (ES) cells. We define four major classes of DNA-binding proteins (Core, PRC, MYC and CTCF) based on their target co-occupancy, and discover reciprocal regulation between the MYC and PRC classes for the activity of nearly all genes under the control of the CpG island (CGI)-containing promoters. This CGI-dependent regulatory mode explains the functional segregation between CGI-containing and CGI-less genes during early development. By defining active enhancers based on the co-occupancy of the Core class, we further demonstrate their additive roles in CGI-containing gene expression and cell type-specific roles in CGI-less gene expression. Altogether, our analyses provide novel insights into previously unknown CGI-dependent global gene regulatory modes.
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