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E-GEOD-11871 - Transcription profiling of Saccharomyces cerevisiae to investigate the role of rad23/rad4 protein complex in transcription and DNA repair in yeast

Status
Submitted on 24 June 2008, released on 8 June 2009, last updated on 10 June 2011
Organism
Saccharomyces cerevisiae
Samples (12)
Array (1)
Protocols (5)
Description
The Rad23/Rad4 protein complex plays a major role in DNA damage recognition during nucleotide excision repair (NER) in yeast. We recently showed that two distinct pathways contribute to efficient NER in yeast. The first operates independently of de novo protein synthesis and requires a nonproteolytic function of the 19S regulatory complex of the 26S proteasome and Rad23. The second pathway requires de novo protein synthesis, and relies on the activity of a newly identified E3 ubiquitin ligase that ubiquitinates Rad4 in response to UV. Surprisingly, we found that cells deleted of either Rad23 or Rad4 caused reduced Rad4 and Rad23 mRNA levels respectively. We considered the possibility of an unexpected role of Rad23 and Rad4 in regulating the expression of genes involved in the transcriptional response to DNA damage. Gene expression profiling has suggested that Rad23 and Rad4 may function as a complex to affect transcription of a small subset of genes in response to UV damage. To determine how Rad4 and Rad23 contribute to the regulation of these genes, we have examined the occupancy of Rad4/Rad23 in their promoter regions by chromatin immunoprecipitation (ChIP), both in the presence and absence of UV damage. Our preliminary ChIP data suggests that the Rad4/Rad23 complex regulates a set of genes in response to UV light. Experiment Overall Design: We perform arrays on Rad4 single, Rad23 single and Rad4/23 double mutants. Each set has 3 biological repeats. All samples are untreated, mRNA prepared from logarithmically growing cultures.
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-11871.idf.txt
Sample and data relationshipE-GEOD-11871.sdrf.txt
Raw data (1)E-GEOD-11871.raw.1.zip
Processed data (1)E-GEOD-11871.processed.1.zip
Experiment designE-GEOD-11871.biosamples.png, E-GEOD-11871.biosamples.svg
Array designA-AFFY-27.adf.txt
R ExpressionSetE-GEOD-11871.eSet.r
Links