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E-GEOD-34786 - Expression data from HDAC1 and HDAC2 knocked-out mouse oocyte

Status
Released on 31 December 2011, last updated on 9 January 2012
Organism
Mus musculus
Samples (16)
Array (1)
Protocols (8)
Description
Dramatic changes in chromatin structure and histone modification occur during oocyte growth, as well as a global cessation of transcription. The role of histone modifications in these processes is poorly understood. We report the effect of conditionally deleting Hdac1 and Hdac2 on oocyte development. Deleting either gene has little or no effect on oocyte development, whereas deleting both genes results in follicle development arrest at the secondary follicle stage. This developmental arrest is accompanied by substantial perturbation of the transcriptome and a global reduction in transcription even though histone acetylation is markedly increased. There is no apparent change in histone repressive marks but there is a pronounced decrease in histone H3K4 methylation, an activating mark. The decrease in H3K4 methylation is likely due to increased expression of Kdm5b because RNAi-mediated targeting of Kdm5b in double mutant oocytes results in an increase in H3K4 methylation. An increase in TRP53 acetylation also occurs in mutant oocytes and may contribute to the observed increased incidence of apoptosis. Taken together, these results suggest seminal roles of acetylation of histone and non-histone proteins in oocyte development. We used microarrays to detail the global programme of gene expression underlying oocyte development and identified distinct classes of regulated genes during this process. Total RNA was extracted from 80 oocytes isolated from mice 12 days-of-age using the PicoPure RNA kit (Arcturus), amplified with the Ovation Pico WTA system (NuGen), and then fragmented and labeled with the FL-OvationTM cDNA Biotin Module V2 (NuGen). Four independent biological replicates were hybridized to Affymetrix GeneChip Mouse 1.1 ST microarrays (http://www.affymetrix.com/). Raw microarray data were analyzed as previously described using MAS5, GeneSpring v7, SAM and EASE software (56). A 1.4-fold cutoff was used for EASE analysis; four biological replicates provide sufficient statistical power and confidence to detect a 1.4-fold change in transcript abundance
Experiment type
transcription profiling by array 
Contacts
Eric N Olson, Hua Pan, Pengpeng Ma, Richard M Schultz, Rusty L Montgomery
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-34786.idf.txt
Sample and data relationshipE-GEOD-34786.sdrf.txt
Raw data (1)E-GEOD-34786.raw.1.zip
Processed data (1)E-GEOD-34786.processed.1.zip
Array designA-GEOD-11533.adf.txt
R ExpressionSetE-GEOD-34786.eSet.r
Links