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| Status |
Public on Jan 26, 2010 |
| Title |
Chromatin signature of embryonic pluripotency is established during zygotic genome activation [Danio rerio] |
| Organism |
Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
[PROJECT] After fertilization the embryonic genome is inactive until transcription is initiated during the maternal-zygotic transition (MZT). This universal process coincides with the formation of pluripotent cells, which in mammals can be used to generate embryonic stem (ES) cells. To study the changes in chromatin structure that accompany zygotic genome activation and pluripotency, we mapped the genomic locations of histone H3 modifications before and after MZT in zebrafish embryos. Repressive H3 lysine 27 trimethylation (H3K27me3) and activating H3 lysine 4 trimethylation (H3K4me3) are only detected after MZT. H3K4me3 marks more than 80% of genes, including many developmental regulatory genes that are also occupied by H3K27me3. Sequential chromatin immunoprecipitation demonstrates that both methylation marks occupy the same promoter regions, revealing that the bivalent chromatin domains found in cultured ES cells also exist in embryos. In addition, we find a large group of genes that are monovalently marked by H3K4me3 but not H3K27me3. These H3K4me3 monovalent genes are neither expressed nor stably bound by RNA polymerase II. Closer inspection of in vitro data sets reveals similar monovalent H3K4me3 domains in ES cells. The analysis of an inducible transgene indicates that H3K4me3 domains can form in the absence of sequence-specific transcriptional activators or stable association with RNA pol II. These results suggest that bivalent and monovalent domains might poise embryonic genes for activation and that the chromatin profile associated with pluripotency is established during MZT.
[SAMPLES] ChIPchip analysis of histone modifications (H3K4me3, H3K27me3, H3K36me3) and RNA polymerase II in pre MZT (256-cell) and post MZT (4hpf; dome/30% epiboly) wt zebrafish embryos.
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| Overall design |
H3K4me3, H3K27me3, H3K36me3 and PolII ChIP-chip at 256 cell stage (one replicate) and 4hpf (dome/30% epiboly) (two replicates)
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| Contributor(s) |
Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, Liu XS, Rinn J, Schier A |
| Citation(s) |
20336069 |
| Submission date |
Jan 25, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Yong Zhang |
| Organization name |
Tongji University
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| Street address |
1239 Siping Road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platforms (1) |
| GPL9970 |
NimbleGen Danio rerio 385K Zv7 tiling array |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA124103 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE20023_RAW.tar |
196.2 Mb |
(http)(custom) |
TAR (of PAIR, WIG) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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