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Schizosaccharomyces pombe

ABSTRACT: The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly [small RNA]

PROVIDER: PRJNA382810 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5445670.fastq.gz	Fastqsanger.gz
	SRR5445680.fastq.gz	Fastqsanger.gz
	SRR5445671.fastq.gz	Fastqsanger.gz
	SRR5445681.fastq.gz	Fastqsanger.gz
	SRR5445672.fastq.gz	Fastqsanger.gz

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Schizosaccharomyces pombe

Project description:The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly [RNA-seq]

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The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly

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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.

2010-09-25 | GSE24360 | GEO

The Dynamic Transcriptome of Schizosaccharomyces pombe Revealed by RNA/DNA Hybrid Mapping

Project description:We determined the strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA/DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA/DNA hybrid to detect RNA molecules hybridized to a high density DNA oligonucleotide tiling microarray. HybMap exhibited exceptional dynamic range and reproducibility, and clearly revealed coding, non-coding and structural RNAs, as well as new RNAs conserved in distant yeast species. Virtually the entire euchromatic genome (including intergenics) is transcribed, with heterochromatin dampening intergenic transcription. Transcriptomes of alternative growth conditions reveal changes in both coding and non-coding RNAs. Interestingly, our analysis reveals large numbers of non-coding RNAs, extensive antisense transcription, new properties of antisense transcripts, and induced divergent transcription. Furthermore, HybMap informed the efficiency and locations of RNA splicing genome-wide. Finally, a remarkable feature is observed at heterochromatin boundaries inside centromeres; strand-specific transcription islands around tRNAs. These new features are discussed in terms of organism fitness and transcriptome evolution. Keywords: yeast, gene expression, bioinformatics

2008-06-30 | GSE11619 | GEO

RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Affymetrix]

Project description:RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe. Total RNA from wild type, dcr1M-NM-^T and rpd1M-NM-^T cells; 3 biological replicates for each strain.

2014-01-23 | E-GEOD-54190 | biostudies-arrayexpress

RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Affymetrix]

2014-01-23 | GSE54190 | GEO

RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Illumina Genome Analyzer]

2014-01-23 | E-GEOD-54194 | biostudies-arrayexpress