 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 15, 2009 |
| Title |
A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos |
| Organism |
Xenopus tropicalis |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis. Here, we report on the epigenetic and transcriptome genome-wide maps of gastrula-stage Xenopus tropicalis embryos using massive parallel sequencing of cDNA (RNA-seq) and DNA obtained by chromatin immunoprecipitation (ChIP-seq) of histone H3 K4 and K27 trimethylation and RNA Polymerase II (RNAPII). These maps identify promoters and transcribed regions. Strikingly, genomic regions featuring opposing histone modifications are mostly transcribed, reflecting spatially regulated expression rather than bivalency as determined by expression profile analyses, sequential ChIP, and ChIP-seq on dissected embryos. Spatial differences in H3K27me3 deposition are predictive of localized gene expression. Moreover, the appearance of H3K4me3 coincides with zygotic gene activation, whereas H3K27me3 is predominantly deposited upon subsequent spatial restriction or repression of transcriptional regulators. These results reveal a hierarchy in the spatial control of zygotic gene activation.
|
| |
|
| Overall design |
ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos
|
| |
|
| Contributor(s) |
Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Françoijs K, Stunnenberg HG, Veenstra GJ |
| Citation(s) |
19758566 |
| |
| Submission date |
Dec 17, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
|
| Phone |
+31 24 3610541
|
| Organization name |
Radboud University
|
| Department |
Molecular Developmental Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL9405 |
Illumina Genome Analyzer (Xenopus (Silurana) tropicalis) |
|
| Samples (4)
|
|
| Relations |
| BioProject |
PRJNA112449 |
| SRA |
SRP001343 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE14025_RAW.tar |
133.9 Mb |
(http)(custom) |
TAR (of BED, TXT) |
| GSE14025_README_bed.txt |
496 b |
(ftp)(http) |
TXT |
| GSE14025_README_expression_level.txt |
300 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...