Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO Fermentable and Nonfermentable Carbon Sources

摘要

Cellular metabolism can change the potency of a chemical’s tumorigenicity. 4-nitroquinoline-1-oxide (4NQO) is a tumorigenic drug widely used on animal models for cancer research. Polymorphisms of the transcription factor confer different levels of resistance to 4NQO in Saccharomyces cerevisiae. To study how different alleles regulate gene expression leading to resistance, transcriptomes of three isogenic S. cerevisiae strains carrying different alleles were profiled via RNA sequencing (RNA-Seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) in the presence and absence of 4NQO. In response to 4NQO, all alleles of drove the expression of (a multidrug transporter), which was highest in the presence of 4NQO resistance-conferring alleles, and overexpression of alone was sufficient to overcome 4NQO-sensitive growth. Using shape metrics to refine the ChIP-Seq peaks, strongly associated with three loci including . In addition to a known target , also bound upstream of ; however, overexpression of these genes did not confer 4NQO resistance. RNA-Seq data also implicated nucleotide synthesis pathways including the de novo purine pathway, and the ribonuclease reductase pathways were downregulated in response to 4NQO. Conversion of a 4NQO-sensitive allele to a 4NQO-resistant allele by a single point mutation mimicked the 4NQO-resistant allele in phenotype, and while the 4NQO resistant allele increased the expression of the ADE genes in the de novo purine biosynthetic pathway, the mutant increased expression of ADE genes even in the absence of 4NQO. These same ADE genes were only increased in the wild-type alleles in the presence of 4NQO, indicating that the point mutation activated to upregulate a pathway normally only activated in response to stress. The various alleles also influenced growth on different carbon sources by altering the function of the mitochondria. Hence, the complement to 4NQO resistance was poor growth on nonfermentable carbon sources, which in turn varied depending on the allele of expressed in the isogenic yeast. The oxidation state of the yeast affected the 4NQO toxicity by altering the reactive oxygen species (ROS) generated by cellular metabolism. The integration of RNA-Seq and ChIP-Seq elucidated how href="http://www.yeastgenome.org/locus/S000005688/overview" data-ga-action="click_feat_suppl" ref="reftype=extlink&article-id=5919752&issue-id=307938&journal-id=1684&FROM=Article%7CFront%20Matter&TO=External%7CLink%7CURI" target="_blank">Yrr1 regulates global gene transcription in response to 4NQO and how various href="http://www.yeastgenome.org/locus/S000005688/overview" data-ga-action="click_feat_suppl" ref="reftype=extlink&article-id=5919752&issue-id=307938&journal-id=1684&FROM=Article%7CFront%20Matter&TO=External%7CLink%7CURI" target="_blank">Yrr1 alleles confer differential resistance to 4NQO. This study provides guidance for further investigation into how href="http://www.yeastgenome.org/locus/S000005688/overview" data-ga-action="click_feat_suppl" ref="reftype=extlink&article-id=5919752&issue-id=307938&journal-id=1684&FROM=Article%7CFront%20Matter&TO=External%7CLink%7CURI" target="_blank">Yrr1 regulates cellular responses to 4NQO, as well as transcriptomic resources for further analysis of transcription factor variation on carbon source utilization.