Schizosaccharomyces pombe
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ABSTRACT:
PROVIDER: PRJNA354589 | ENA |
REPOSITORIES: ENA
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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
Project description:Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin [MNase-Seq]
| PRJNA174085 | ENA
Project description:Recent studies have revealed that eukaryotic genomes are pervasively transcribed by RNA polymerase II, producing a plethora of non-coding RNAs which frequently overlap protein-coding genes. Despite the fact that overlapping transcription is well known to repress transcription initiation from downstream promoters, the mechanism behind this phenomenon has remained elusive. It was proposed that transcriptional interference relies on the act of transcription rather than the RNA itself to block access of the transcription machinery to downstream promoters. Here, we use the fission yeast Schizosaccharomyces pombe to demonstrate that an RNA and chromatin-dependent mechanism is responsible for transcriptional interference. This relies on co-transcriptional recruitment of the histone deacetylase Clr3 to nascent non-coding RNA, leading to formation of hypoacetylated chromatin and repression of the downstream protein-coding gene. Our findings highlight the unexpected requirement for RNA as well as trans-acting protein factors in mediating the repressive effects imposed on gene expression through overlapping non-coding transcription.
2018-03-20 | GSE104713 | GEO
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 The dynamic transcriptome of S.pombe was determined using a whole genome tiling array hybridized to total RNA. Transcripts were detected using an antibody specific to RNA/DNA hybrids. This technique, called HybMap, was used across three different growth conditions (Heat shock, MMS treatment, and minimal media) in addtion to standard conditions. To further understand the transcriptome, we isolated PolyA RNA from S.pombe grown in standard conditions and used the HybMap method. Finally, the transcriptome was compared to Pol II, histone, and H3K36me3 ChIP occupancy. NOTE: Processed microarray data values listed in this repository represent only those probes that align to unique genomic positions. Probes that align to multiple genomic locations (reported in the Platform description) may not have values. Please refer to the web link above for a complete genomic data set.
2008-06-29 | E-GEOD-11619 | biostudies-arrayexpress
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
Project description:A global non coding RNA system modulates fission yeast protein levels in response to stress
| PRJNA244471 | ENA
Project description:RNA interference is essential for cellular quiescence (S. pombe)
| PRJNA341984 | ENA
Project description:A chromatin-based mechanism for limiting divergent non-coding transcription
| PRJNA227340 | ENA
Project description:fission yeast meiotic drive recombination mapping
| PRJNA376152 | ENA
Project description:The metazoan nuclear periphery is involved in transcriptional regulation and chromatin organisation. To test whether this is also the case in the fission yeast Schizosaccharomyces pombe, we performed DamID experiments with two inner nuclear membrane (INM) proteins, Ima1 and Man1. The resulting map showed that about a third of the genome is associated with the nuclear periphery. We find that both INM proteins preferentially associate with lowly expressed genes, and are depleted from highly expressed genes. Further, intergenic regions of divergent gene pairs are more frequently associated with the periphery than convergent pairs, indicating that transcription points away from the periphery rather than toward it
2012-01-18 | GSE30476 | GEO