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Ludwig Institute/UCSD ENCODE project June 2007 Release

ABSTRACT: The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication. Keywords: ChIP-chip ENCODE

ORGANISM(S): Homo sapiens

PROVIDER: GSE7872 | GEO | 2007/06/01

REPOSITORIES: GEO

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Project description:Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). We integrated CAGE-seq, ChIP-seq and gene expression profiles to discover shared or cell-specific regulatory elements, transcription start sites and transcripts associated to the transition from pluripotent to neural-restricted stem cell. Our analysis showed that >90% of the promoters are in common between the two cell types, while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provide a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and gene expression programs occurring in the transition from a pluripotent to a neural-restricted cell fate. Genome-wide mapping of H3K4me1 and H3K4me3 in NESCs ChIP-seq for H3K4me1 and H3K4me3 in NESCs

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Ludwig Institute/UCSD ENCODE project June 2007 Release

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