CpG island-mediated global gene regulatory modes in mouse embryonic stem cells

Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of >200 large sequencing data sets to elucidate the regulatory logic of global gene expression programs in mouse embryonic stem (ES) cells. We defin...

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Bibliographic Details
Published in:	Nature communications 2014-11, Vol.5 (1), p.5490-5490, Article 5490
Main Authors:	Beck, Samuel, Lee, Bum-Kyu, Rhee, Catherine, Song, Jawon, Woo, Andrew J, Kim, Jonghwan
Format:	Article
Language:	eng
Subjects:	Animals Base Sequence Cell Line CpG Islands - genetics DNA Methylation - genetics DNA-Binding Proteins - classification DNA-Binding Proteins - genetics Embryonic Stem Cells - cytology Enhancer Elements, Genetic - genetics Gene Expression Regulation - genetics Genes, Regulator Mice Polycomb-Group Proteins - genetics Promoter Regions, Genetic Proto-Oncogene Proteins c-myc - genetics Sequence Analysis, DNA
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Summary:	Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of >200 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.
ISSN:	2041-1723 2041-1723