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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 [gene expression profile] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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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.
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| Overall design |
ESCs (H9 NIH code WA09, ISL1 Ds-Red) were kindly provided by the group of K.R. Chien. Neural differentiation was induced by the method of embryoid bodies following a published protocol [1]. Briefly, 4-days embryoid bodies were transferred to polyornithine-coated dishes and propagated in N2-supplemented DMEM/F12 (Invitrogen). Total RNA was extracted from 1-2x10^6 cells from three different cultures of ESCs and NESCs, transcribed into biotinylatedcRNA and hybridized onto GeneChip® HG-U133 Plus 2.0 Arrays (Affymetrix) according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA).
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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 23, 2015 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
[email protected]
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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) |
| GPL19171 |
Affymetrix GeneChip Human Genome U133 Array Set HG-U133 Plus2 based on a custom CDF (GeneAnnot version 2.2.0) |
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| Samples (6)
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| GSM1501178 |
Human embryonic stem cells (H9), replicate A |
| GSM1501179 |
Human embryonic stem cells (H9), replicate B |
| GSM1501180 |
Human embryonic stem cells (H9), replicate C |
| GSM1501181 |
ESC-derived neural precursors, replicate A |
| GSM1501182 |
ESC-derived neural precursors, replicate B |
| GSM1501183 |
ESC-derived neural precursors, replicate C |
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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 |
PRJNA260623 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61266_RAW.tar |
40.3 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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