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Vol. 9, Issue 8, 775-792, August 1999

METHODS
Candidate Regulatory Sequence Elements for Cell Cycle-Dependent Transcription in Saccharomyces cerevisiae

Tyra G. Wolfsberg,1,4 Andrei E. Gabrielian,1,4 Michael J. Campbell,2 Raymond J. Cho,3 John L. Spouge,1 and David Landsman1,5

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 USA; 2 Molecular Applications Group, Palo Alto, California 94304 USA; 3 Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 USA

Recent developments in genome-wide transcript monitoring have led to a rapid accumulation of data from gene expression studies. Such projects highlight the need for methods to predict the molecular basis of transcriptional coregulation. A microarray project identified the 420 yeast transcripts whose synthesis displays cell cycle-dependent periodicity. We present here a statistical technique we developed to identify the sequence elements that may be responsible for this cell cycle regulation. Because most gene regulatory sites contain a short string of highly conserved nucleotides, any such strings that are involved in gene regulation will occur frequently in the upstream regions of the genes that they regulate, and rarely in the upstream regions of other genes. Our strategy therefore utilizes statistical procedures to identify short oligomers, five or six nucleotides in length, that are over-represented in upstream regions of genes whose expression peaks at the same phase of the cell cycle. We report, with a high level of confidence, that 9 hexamers and 12 pentamers are over-represented in the upstream regions of genes whose expression peaks at the early G1, late G1, S, G2, or M phase of the cell cycle. Some of these sequence elements show a preference for a particular orientation, and others, through a separate statistical test, for a particular position upstream of the ATG start codon. The finding that the majority of the statistically significant sequence elements are located in late G1 upstream regions correlates with other experiments that identified the late G1/early S boundary as a vital cell cycle control point. Our results highlight the importance of MCB, an element implicated previously in late G1/early S gene regulation, as most of the late G1 oligomers contain the MCB sequence or variations thereof. It is striking that most MCB-like sequences localize to a specific region upstream of the ATG start codon. Additional sequences that we have identified may be important for regulation at other phases of the cell cycle.

[A companion website to this manuscript is available from http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/Cell_cycle_data]

4   These authors contributed equally to this work.
5   Corresponding author.

9:775-792 ©1999 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/99 $5.00
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