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Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae
T G Wolfsberg1, A E Gabrielian, M J Campbell
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
Genome Research
|August 14, 1999
Summary
Researchers developed a statistical method to find DNA sequence elements regulating gene expression across the cell cycle. This analysis identified specific DNA oligomers, including MCB, crucial for cell cycle control in yeast.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Genome-wide transcript monitoring generates vast gene expression data.
- Predicting transcriptional coregulation requires identifying regulatory elements.
- Cell cycle-dependent gene expression is fundamental to cellular processes.
Purpose of the Study:
- To develop a statistical technique for identifying DNA sequence elements responsible for cell cycle-dependent transcriptional regulation.
- To analyze upstream regions of yeast genes with cell cycle-periodic expression.
- To discover short oligomers over-represented in specific cell cycle phases.
Main Methods:
- Statistical identification of short nucleotide oligomers (5-6 nucleotides) in gene upstream regions.
- Analysis of 420 yeast transcripts showing cell cycle-dependent periodicity.
- Utilizing over-representation analysis to find regulatory sequence elements.
Main Results:
- Identified 9 hexamers and 12 pentamers over-represented in upstream regions of cell cycle-regulated genes.
- Found sequence elements with preferences for orientation and position relative to the ATG start codon.
- Confirmed the importance of MCB (M-phase Cell Cycle Box) and its variations, particularly in late G1.
- Observed that most MCB-like sequences are located in a specific upstream region.
Conclusions:
- The developed statistical method effectively identifies regulatory sequence elements involved in cell cycle control.
- The identified oligomers, including MCB, play significant roles in regulating gene expression at specific cell cycle phases.
- The localization of regulatory elements to specific upstream regions provides insights into transcriptional control mechanisms.
- Further investigation of identified sequences may reveal novel regulatory elements for other cell cycle phases.
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