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Analysis of Saccharomyces cerevisiae genome for the distributions of stress-response elements potentially affecting gene expression by transcriptional interference.
In Silico Biol. 2009; 9(5-6):379-89.SB

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.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Liu Y
Computer and Information Science Department, Gannon University, Erie, PA, USA.
Ye S
No affiliation info available
Erkine AM
No affiliation info available

MeSH

ApoptosisBase SequenceBinding SitesDown-RegulationGene Expression Regulation, FungalGenes, FungalGenome, FungalHeat-Shock ResponseHydrogen BondingModels, GeneticMolecular Sequence DataOpen Reading FramesResponse ElementsSaccharomyces cerevisiaeStress, PhysiologicalTranscription, Genetic

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

22430439

Citation

Liu, Yunkai, et al. "Analysis of Saccharomyces Cerevisiae Genome for the Distributions of Stress-response Elements Potentially Affecting Gene Expression By Transcriptional Interference." In Silico Biology, vol. 9, no. 5-6, 2009, pp. 379-89.
Liu Y, Ye S, Erkine AM. Analysis of Saccharomyces cerevisiae genome for the distributions of stress-response elements potentially affecting gene expression by transcriptional interference. In Silico Biol. 2009;9(5-6):379-89.
Liu, Y., Ye, S., & Erkine, A. M. (2009). Analysis of Saccharomyces cerevisiae genome for the distributions of stress-response elements potentially affecting gene expression by transcriptional interference. In Silico Biology, 9(5-6), 379-89. https://doi.org/10.3233/ISB-2009-0412
Liu Y, Ye S, Erkine AM. Analysis of Saccharomyces Cerevisiae Genome for the Distributions of Stress-response Elements Potentially Affecting Gene Expression By Transcriptional Interference. In Silico Biol. 2009;9(5-6):379-89. PubMed PMID: 22430439.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis of Saccharomyces cerevisiae genome for the distributions of stress-response elements potentially affecting gene expression by transcriptional interference. AU - Liu,Yunkai, AU - Ye,Sujuan, AU - Erkine,Alexandre M, PY - 2012/3/21/entrez PY - 2009/1/1/pubmed PY - 2013/10/1/medline SP - 379 EP - 89 JF - In silico biology JO - In Silico Biol VL - 9 IS - 5-6 N2 - 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. SN - 1434-3207 UR - https://www.unboundmedicine.com/medline/citation/22430439/Analysis_of_Saccharomyces_cerevisiae_genome_for_the_distributions_of_stress_response_elements_potentially_affecting_gene_expression_by_transcriptional_interference_ L2 - https://www.yeastgenome.org/reference/22430439 DB - PRIME DP - Unbound Medicine ER -