E-GEOD-20137 - Gene expression in unfertilized eggs and the MBT stage of zebrafish embryos

Status
Submitted on 1 February 2010, released on 14 May 2010, last updated on 10 June 2011
Organism
Danio rerio
Samples (7)
Array (1)
Protocols (8)
Description
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. 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.
Experiment type
transcription profiling by array 
Contacts
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-20137.idf.txt
Sample and data relationshipE-GEOD-20137.sdrf.txt
Raw data (1)E-GEOD-20137.raw.1.zip
Processed data (1)E-GEOD-20137.processed.1.zip
Array designA-GEOD-9998.adf.txt
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