Analysis of Saccharomyces cerevisiae Genome
for the Distributions of Stress-Response Elements Potentially Affecting Gene
Expression by Transcriptional Interference
Affiliations: Computer and Information Science Department, Gannon
University, Erie, PA, USA | Department of Computer Science, University of South
Dakota, Vermillion, SD, USA | College of Pharmacy and Health Sciences, Butler
University, Indianapolis, IN, USA
Note: [] Corresponding author: A.M. Erkine, College of Pharmacy and
Health Sciences, Butler University, 4600 Sunset Avenue, Indianapolis, IN 46208,
USA. Tel.: +1 317 940 8569; Fax: +1 317 940 6172; E-mail: [email protected]
Abstract: Cellular stress responses are characterized by coordinated
transcriptional induction of genes encoding a group of conserved proteins known
as molecular chaperones, most of which are also known as heat shock proteins
(HSPs). In S. cerevisiae, transcriptional responses to stress are
mediated via two trans-regulatory activators: heat shock
transcription factors (HSFs) that bind to heat shock elements (HSEs), and the
Msn2 and Msn4 transcription factors that bind to stress response elements
(STREs). Recent studies in S. cerevisiae demonstrated that a significant
portion of the non-coding region in the genome is transcribed and this
intergenic transcription could regulate the transcription of adjacent genes by
transcription interference. The goal of this study was to analyze the genomic
distribution of HSF and Msn2/4 binding sites and to study the potential for
transcription interference regulated by stress response systems. Our
genome-wide analysis revealed that 297 genes have STREs in their promoter
region, whereas 310 genes contained HSEs. Twenty-five genes had both HSEs and
STREs in their promoters. The first set of genes is potentially regulated by
the Msn2/Msn4/STRE interaction. For the second set of genes, regulation by heat
shock could be mediated through HSF/HSE regulatory mechanisms. The overlap
between these groups suggests a co-regulation by the two pathways. Our study
yielded 239 candidate genes, whose regulation could potentially be affected by
heat-shock via transcription interference directed both from upstream and
downstream areas relative to the native promoters. In addition we have
categorized 924 genes containing HSE and/or STRE elements within the Open
Reading Frames (ORFs), which may also affect normal transcription. Our study
revealed a widespread possibility for the regulation of genes via
transcriptional interference initiated by stress response. We provided a
categorization of genes potentially affected at the transcriptional level by
known stress-response systems.
