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| Status |
Public on May 21, 2015 |
| Title |
Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [CAGE-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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
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| Overall design |
ESCs and NESCs promoter usage profiling by CAGE-seq
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| Contributor(s) |
Poletti V, Carri AD, Tagliazucchi GM, Petiti L, Mazza EM, Peano C, De Bellis G, Bicciato S, Miccio A, Cattaneo E, Mavilio F |
| Citation(s) |
25978676 |
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| Submission date |
Sep 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
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| Phone |
+39-049-827-6108
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| Organization name |
University of Padova
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| Department |
Molecular Medicine
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| Street address |
via U. Bassi 59/b
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| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (1) |
| GSM1501174 |
Level 2 promoters in human ESCs and NESCs |
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| This SubSeries is part of SuperSeries: |
| GSE61267 |
Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells |
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| Relations |
| BioProject |
PRJNA260622 |
| SRA |
SRP046749 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61264_RAW.tar |
160.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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