Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

ABSTRACT: Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells. CAGE library construction from RNA extracted from control and exosome-depleted cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Robin Andersson

PROVIDER: E-GEOD-58991 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

Andersson Robin R Refsing Andersen Peter P Valen Eivind E Core Leighton J LJ Bornholdt Jette J Boyd Mette M Heick Jensen Torben T Sandelin Albin A

Nature communications 20141112

Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. Although recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protein-coding (pc) genes, limited progress has been made in distinguishing functional RNA from spurious transcription events. This is partly due to present RNA classification, which is typically based on tech ...[more]

PMID: 25387874

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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. Investiagtion of promoters usage changes during ESCs neural induction ESCs and NESCs promoter usage profiling by CAGE-seq

Dataset Information

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Publications

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

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