A novel cis-acting element required for DNA damage-inducible expression of yeast DIN7

The current state of eukaryotic DNA base damage and repair

DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair.

Genotoxicity of Chemical Compounds Identification and Assessment by Yeast Cells Transformed With GFP Reporter Constructs Regulated by the PLM2 or DIN7 Promoter

Yeast cells transformed with high-copy number plasmids comprising a green fluorescent protein (GFP)-encoding gene optimized for yeast under the control of the new DIN7 or PLM2 and the established RNR2 and RAD54 promoters were used to assess the genotoxic potential of chemical compounds. The activity of potential DNA-damaging agents was investigated by genotoxicity assays and by OxoPlate assay in the presence of various test compounds. The fluorescence signal generated by GFP in response to DNA damage was related to the different concentrations of analytes and the analyte-dependent GFP synthesis. The use of distinct DNA damage-inducible promoters presents alternative genotoxicity testing strategies by selective induction of promoters in response to DNA damage. The new DIN7 and PLM2 systems show higher sensitivity than the RNR2 and RAD54 systems in detecting 4-nitroquinoline- N-oxide and actinomycin D. Both DIN7 and PLM2 systems are able to detect camptothecin while RNR2 and RAD54 systems are not. Automated laboratory systems with assay performance on 384-well microplates provide for cost-effective high-throughput screening of DNA-damaging agents, reducing compound consumption to about 53% as compared with existing eukaryotic genotoxicity bioassays.

Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets

Unraveling the temporal complexity of cellular systems is a challenging task, as the subtle coordination of molecular activities cannot be adequately captured by simple mathematical concepts such as correlation. This paper addresses the challenge with a data-mining approach. We introduce the novel concept of a "frequent temporal association pattern" (FTAP): a set of genes simultaneously exhibit complex temporal expression patterns recurrently across multiple microarray datasets. Such temporal signals are hard to identify in individual microarray datasets, but become significant by their frequent occurrences across multiple datasets. We designed an efficient two-stage algorithm to identify FTAPs. First, for each gene we identify expression trends that occur frequently across multiple datasets. Second, we look for a set of genes that simultaneously exhibit their respective trends recurrently in multiple datasets. We applied this algorithm to 18 yeast time-series microarray datasets. The majority of FTAPs identified by the algorithm are associated with specific biological functions. Moreover, a significant number of patterns include genes that are functionally related but do not exhibit co-expression; such gene groups cannot be captured by clustering algorithms. Our approach offers advantages: (1) it can identify complex associations of temporal trends in gene expression, an important step towards understanding the complex mechanisms governing cellular systems; (2) it is capable of integrating time-series data with different time scales and intervals; and (3) it yields results that are robust against outliers.

The yeast checkpoint kinase Dun1 downregulates DIN7 in the absence of DNA damage

Yeast DIN7 is a DNA damage-inducible gene. Its expression is increased in the absence of Dun1, a DNA damage checkpoint kinase. We identified a DIN7 promoter region responsible for Dun1-mediated downregulation and found that DIN7 expression was not further increased in response to hydroxyurea in Deltadun1 cells. Thus DIN7 repression by Dun1 can be released upon DNA damage.