E-GEOD-42971 - The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (H2O2)

Status
Released on 24 July 2013, last updated on 5 September 2013
Organism
Saccharomyces cerevisiae
Samples (18)
Protocols (4)
Description
Snt2 is a yeast chromatin-interacting protein whose function has not been well characterized, that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we show that in response to H2O2, Snt2 and Ecm5 colocalize to promoters of genes involved in various aspects of the environmental stress response. By integrating these ChIP-seq results with expression analysis, we identify a key set of target genes that require Snt2 for proper expression after H2O2 stress. Finally, by mapping Snt2 and Ecm5 localization before and after rapamycin treatment, we identify a subset of H2O2-specific Snt2 and Ecm5 target promoters that are also targeted in response to rapamycin. Our results establish a function for Snt2 in regulating transcriptional changes in response to oxidative stress, and suggest Snt2 may have a role in additional stress pathways. Crosslinking ChIP analysis to identify sites of Snt2 or Ecm5 genomic localization before, 0.5 hours after, or 4 hours after treatment with H2O2 (final concentration 0.4 mM). Snt2 and Ecm5 were genomically tagged with a 13Myc tag at their C termini. ChIPs were performed using a Myc antibody on either Snt2-Myc or Ecm5-Myc strains, or on an untagged wildtype strain (BY4741) as a control. Inputs and ChIPs from untagged strain were sequenced as controls.
Experiment type
ChIP-seq 
Contacts
David Allis <geo@ncbi.nlm.nih.gov>, Beatrix M Ueberheide, Brian T Chait, C D Allis, Deyou Zheng, Lindsey A Baker, Scott Dewell
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-42971.idf.txt
Sample and data relationshipE-GEOD-42971.sdrf.txt
Processed data (1)E-GEOD-42971.processed.1.zip
Links