Unknown,Transcriptomics,Genomics,Proteomics

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


ABSTRACT: In order to identify the regions occupied by transcription factors, we performed bio-ChIP followed by massive parallel sequencing (bioChIP-Seq) in mouse ES cells. A total of seven DNA transcription factors including Myc module (Myc, Max, E2F4, Tip60 and Dmap1) and Core module transcription factors (Nanog, Dax1; Kim et al., 2010) were identified. We show that the transcription factors can be classified into several classes according to their occupancies. Our data also show transcription factors in the same class co-occupy the same regulatory elements, share the common characteristics and act together. Identification of seven transcription factor binding sites in mES cells

ORGANISM(S): Mus musculus

SUBMITTER: Jonghwan Kim 

PROVIDER: E-GEOD-48666 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Beck Samuel S   Lee Bum-Kyu BK   Rhee Catherine C   Song Jawon J   Woo Andrew J AJ   Kim Jonghwan J  

Nature communications 20141118


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 al  ...[more]

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