Transcriptome profiling of Saccharomyces cerevisiae mutants lacking C2H2 zinc finger proteins

<p>Abstract</p> <p>Background</p> <p>The budding yeast <it>Saccharomyces cerevisiae</it> 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, <it>ypr013cΔ,</it><it>ypr015cΔ</it> and <it>ypr013cΔypr015cΔ</it>.</p> <p>Results</p> <p>Gene expression patterns were remarkably different between wild type and the mutants. The results indicate altered expression of 79 genes in<it> ypr013</it>cΔ, 185 genes in <it>ypr015</it>cΔ 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.</p> <p>Conclusion</p> <p>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.</p

Transcriptome Profiling of \u3ci\u3eSaccharomyces cerevisiae\u3c/i\u3e Mutants Lacking C2H2 Zinc Finger Proteins

BackgroundThe 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. ResultsGene expression patterns were remarkably different between wild type and the mutants. The results indicate altered expression of 79 genes in ypr013 cΔ, 185 genes in ypr015 cΔ 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. ConclusionOur 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

Identification of MicroRNAs in Bovine Spermatozoa with Implications of Fertility

MicroRNAs are small RNA molecules that could possibly play a major role in fertility. In the experiment, spermatozoa were extracted from bovine followed by an extraction of total RNA. Bovine spermatozoa were extracted from two bulls of different fertility, high and low fertility. An expression array was done to compare the expression levels of the microRNAs. It was shown that thousands of microRNAs are present in bovine spermatozoa but only a small amount was significantly expressed. The microRNAs from low fertility bulls were more highly expressed than those in high fertility bulls. A Bioanalyzer gel was used to confirm the results of the microarray data. The microRNAs were present in the bull’s spermatozoa at 25 nucleotides. The functions of the significantly expressed microRNAs are not known but there is a great possibility that their functions affect fertility

RESEARCH Dynamics of microRNAs in bull spermatozoa Open Access

Background: MicroRNAs are small non-coding RNAs that regulate gene expression and thus play important roles in mammalian development. However, the comprehensive lists of microRNAs, as well as, molecular mechanisms by which microRNAs regulate gene expression during gamete and embryo development are poorly defined. The objectives of this study were to determine microRNAs in bull sperm and predict their functions. Methods: To accomplish our objectives we isolated miRNAs from sperm of high and low fertility bulls, conducted microRNA microarray experiments and validated expression of a panel of microRNAs using real time RT-PCR. Bioinformatic approaches were carried out to identify regulated targets. Results: We demonstrated that an abundance of microRNAs were present in bovine spermatozoa, however, only seven were differentially expressed; hsa-aga-3155,-8197,-6727,-11796,-14189,-6125,-13659. The abundance of miRNAs in the spermatozoa and the differential expression in sperm from high vs. low fertility bulls suggests that the miRNAs possibly play important functions in the regulating mechanisms of bovine spermatozoa. Conclusion: Identification of specific microRNAs expressed in spermatozoa of bulls with different fertility phenotypes will help better understand mammalian gametogenesis and early development