E-GEOD-19634 - Gene Expression of MATa yeast segregants (YJM789 X S96) after alpha factor treatment

Submitted on 23 December 2009, released on 14 May 2010, last updated on 10 June 2011
Saccharomyces cerevisiae
Samples (48)
Array (1)
Protocols (9)
In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c, as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. We showed that the majority of TF binding variation is cis-linked and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several known and proposed Ste12 cofactors. We also identified two trans factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than 10 genes under α-factor treatment. Neither of these two genes was known to regulate Ste12 previously, and we suggest that they may be key mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes, indicating that binding variation is functional. Many of the variable bound genes are involved in cell wall organization and biogenesis. Overall, we identified key regulators of molecular diversity among individuals and provide novel insights into mechanisms of gene regulation. We measured gene expression levels after 30 minutes treatment with alpha factor for 43 MATa segregants from a YJM789 X S96 cross, as well as MATa parental lines. We also measured the gene expression levels without alpha factor treatment for parental lines (S96, HS959) and SEG8 as controls.
Experiment type
transcription profiling by array 
Wei Zheng <wei.zheng@yale.edu>, Eugenio Mancera, Hongyu Zhao, Lars Steinmetz, Michael Snyder
Investigation descriptionE-GEOD-19634.idf.txt
Sample and data relationshipE-GEOD-19634.sdrf.txt
Raw data (1)E-GEOD-19634.raw.1.zip
Processed data (1)E-GEOD-19634.processed.1.zip
Array designA-GEOD-9825.adf.txt