title: Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression.
abstract: This report provides a global view of how gene expression is affected by DNA replication. We analyzed synchronized cultures of Saccharomyces cerevisiae under conditions that prevent DNA replication initiation without delaying cell cycle progression. We use a higher-order singular value decomposition to integrate the global mRNA expression measured in the multiple time courses, detect and remove experimental artifacts and identify significant combinations of patterns of expression variation across the genes, time points and conditions. We find that, first, approximately 88% of the global mRNA expression is independent of DNA replication. Second, the requirement of DNA replication for efficient histone gene expression is independent of conditions that elicit DNA damage checkpoint responses. Third, origin licensing decreases the expression of genes with origins near their 3' ends, revealing that downstream origins can regulate the expression of upstream genes. This confirms previous predictions from mathematical modeling of a global causal coordination between DNA replication origin activity and mRNA expression, and shows that mathematical modeling of DNA microarray data can be used to correctly predict previously unknown biological modes of regulation.
authors.affiliation: Department of Biomedical Engineering, University of Texas, Austin, TX 78712, USA.
authors.forename: Larsson
authors.initials: L
authors.lastname: Omberg
authors.forename: Joel R
authors.initials: JR
authors.lastname: Meyerson
authors.forename: Kayta
authors.initials: K
authors.lastname: Kobayashi
authors.forename: Lucy S
authors.initials: LS
authors.lastname: Drury
authors.forename: John F X
authors.initials: JF
authors.lastname: Diffley
authors.forename: Orly
authors.initials: O
authors.lastname: Alter
mesh_terms: D004261:DNA Replication / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018741:Replication Origin / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D013997:Time Factors
chemical_list: D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins