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Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe

ABSTRACT: Small RNA expression in swi6 mutants, dcr1 delta, and wild type fission yeast Schizosaccharomcyces pombe

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE42849 | GEO | 2013/07/20

SECONDARY ACCESSION(S): PRJNA183638

REPOSITORIES: GEO

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Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe

Project description:Small RNA expression in swi6 mutants, dcr1 delta, and wild type fission yeast Schizosaccharomcyces pombe wild type, swi6 mutant, and dcr1 delta mutant

2013-07-20 | E-GEOD-42849 | biostudies-arrayexpress

DamID for Swi6, Rdp1 and Dcr1 in Schizosaccharomyces pombe

Project description:In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) pathway is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic silencing of centromeric repeats. Here we demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DamID (DNA adenine methyltransferase identification) we show that Dcr1 and Rdp1 physically associate with some euchromatic genes, non-coding RNA (ncRNA) genes, and retrotransposon long terminal repeats (LTRs), and that this association is independent of the Clr4 histone methyltransferase. Physical association of RNAi with chromatin is sufficient to trigger a silencing response but not to assemble heterochromatin. The mode of silencing at the newly identified RNAi targets is consistent with a co-transcriptional gene silencing model as proposed earlier and functions with trace amounts of siRNAs. We anticipate that similar mechanisms could also be operational in other eukaryotes.

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Project description:Imbalances of gene expression in aneuploids containing an abnormal number of chromosomes cause a variety of growth and developmental defects. Aneuploid cells of the fission yeast Schizosaccharomyces pombe are inviable, or very unstable, during mitotic growth. However, S. pombe haploid cells bearing a small portion (less than 20%) of the third chromosome can grow stably as a partial aneuploid. We compared the gene expression profiles of partial aneuploid strains with those of the normal haploid strain using DNA microarray analysis. The expression of genes in disomic or trisomic cells was found to increase approximately in proportion to their copy number. We also found that some genes in the monosomic regions of partial aneuploid strains changed their expression level despite there being no change in copy number. We initially speculated that this change in gene expression was a secondary effect resulting from increased expression of the genes in the disomic or trisomic regions. However, even in an aneuploid strain that bears a minichromosome containing no protein coding genes, genes located within about 50kb of the telomere showed similar increases in expression. This result indicates that the change in expression of the genes in the telomere-adjacent region is not a secondary effect of the increased gene dosage. Examining the distribution of the heterochromoatin protein Swi6 using DNA microarray analysis, we found that binding of Swi6 within ~50kb from the telomere occurred less in partial aneuploid strains compared to euploid strains. These results suggest that additional chromosomes in aneuploid strains could lead to imbalances in gene expression through derepression of heterochromatin. Keywords: Type of experiment: Comparing between partial aneuploid strains and normal haploid strains.

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