Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

CAGE experiment of S. Cerevisiae strain CEN.PK113-7D in four different chemostat conditions

ABSTRACT: The CAGE experiment was performed in four different chemostat conditions to assess if and how much the Transcription start site landscape changes in the industrial relevant S. Cerevisiae strain CEN.PK113-7D in different conditions. CAGE was also used to obtain accurate TSS annotations for each expressed gene.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Christoph Börlin

PROVIDER: E-MTAB-6650 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions.

Börlin Christoph S CS Cvetesic Nevena N Holland Petter P Bergenholm David D Siewers Verena V Lenhard Boris B Nielsen Jens J

FEMS yeast research 20190301 2

One of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of TSSs at four different environmental c ...[more]

PMID: 30590648

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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

CAGE experiment of S. Cerevisiae strain CEN.PK113-7D in four different chemostat conditions

Publications

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions.

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