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| Status |
Public on Feb 03, 2010 |
| Title |
Gene expression in unfertilized eggs and the MBT stage of zebrafish embryos |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by array
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| Summary |
Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. Culture of embryo-derived cells results in a switch from histone acetylation to K9 and K27 trimethylation on genes transcriptionally inactivated, resulting in a profile similar to that of fibroblasts. All promoters retain H3K4me3, indicating no correlation between H3K4me3 occupancy and gene expression. Our results illustrate a complex chromatin state on the promoter of pluripotency-associated genes in the zebrafish embryo, shortly after the embryonic genome is turned on.
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| Overall design |
We assessed gene expression in unfertilized eggs and the MBT stage of zebrafish embryos (~ 3.5 hpf) using a 44K custom designed chip from Agilent (3 and 4 replicates, respectively). Genes of interest were extracted and evaluated according to expression dynamics and levels.
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| Contributor(s) |
Aanes H, Collas P |
| Citation(s) |
20336603 |
| Submission date |
Feb 01, 2010 |
| Last update date |
Jul 12, 2012 |
| Contact name |
Håvard Aanes |
| E-mail(s) |
havard.aanes@nvh.no
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| Organization name |
Norwegian School of Veterinary Science
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| Department |
Biochemistry
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| Street address |
Ullevålsveien 72
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| City |
Oslo |
| State/province |
Oslo |
| ZIP/Postal code |
0883 |
| Country |
Norway |
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| Platforms (1) |
| GPL9998 |
Agilent Dano rerio 44K custom chip [Agilent-021643 Feature number version] |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA125671 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE20137_RAW.tar |
54.7 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE20137_genes_of_interest.txt.gz |
461 b |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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