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This article is part of the supplement: The 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07)

Open Access Research

Transcriptome profiling of Saccharomyces cerevisiae mutants lacking C2H2 zinc finger proteins

Jinghe Mao1*, Tanwir Habib2, Ming Shenwu1, Baobin Kang2, Wilbur Allen1, LaShonda Robertson1, Jack Y Yang3 and Youping Deng2*

Author Affiliations

1 Department of Biology, Tougaloo College, Tougaloo, MS 39174, USA

2 Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA

3 Harvard Medical School, Harvard University, Cambridge, Massachusetts 02140-0888 USA

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BMC Genomics 2008, 9(Suppl 1):S14  doi:10.1186/1471-2164-9-S1-S14

Published: 20 March 2008

Abstract

Background

The budding yeast Saccharomyces cerevisiae is a eukaryotic organism with extensive genetic redundancy. Large-scale gene deletion analysis has shown that over 80% of the ~6200 predicted genes are nonessential and that the functions of 30% of all ORFs remain unclassified, implying that yeast cells can tolerate deletion of a substantial number of individual genes. For example, a class of zinc finger proteins containing C2H2 zinc fingers in tandem arrays of two or three is predicted to be transcription factors; however, seven of the thirty-one predicted genes of this class are nonessential, and their functions are poorly understood. In this study we completed a transcriptomic profiling of three mutants lacking C2H2 zinc finger proteins, ypr013cΔ,ypr015cΔ and ypr013cΔypr015cΔ.

Results

Gene expression patterns were remarkably different between wild type and the mutants. The results indicate altered expression of 79 genes in ypr013cΔ, 185 genes in ypr015cΔ and 426 genes in the double mutant when compared with that of the wild type strain. More than 80% of the alterations in the double mutants were not observed in either one of the single deletion mutants. Functional categorization based on Munich Information Center for Protein Sequences (MIPS) revealed up-regulation of genes related to transcription and down-regulation of genes involving cell rescue and defense, suggesting a decreased response to stress conditions. Genes related to cell cycle and DNA processing whose expression was affected by single or double deletions were also identified.

Conclusion

Our results suggest that microarray analysis can define the biological roles of zinc finger proteins with unknown functions and identify target genes that are regulated by these putative transcriptional factors. These findings also suggest that both YPR013C and YPR015C have biological processes in common, in addition to their own regulatory pathways.