GEO DataSets

(Submitter supplied) RNAseIII ribonucleases act at the heart of RNA silencing pathways by processing precursor RNAs into mature microRNAs and siRNAs. In the fission yeast Schizosaccharomyces pombe, siRNAs are generated by the RNAseIII enzyme Dcr1 and are required for heterochromatin formation. In this study, we have analyzed the subcellular localization of Dcr1 and found that it accumulates in the nucleus and is enriched at the nuclear periphery. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9453

3 Samples

Download data: TAB

(Submitter supplied) RNAseIII ribonucleases act at the heart of RNA silencing pathways by processing precursor RNAs into mature microRNAs and siRNAs. In the fission yeast Schizosaccharomyces pombe, siRNAs are generated by the RNAseIII enzyme Dcr1 and are required for heterochromatin formation. In this study, we have analyzed the subcellular localization of Dcr1 and found that it accumulates in the nucleus and is enriched at the nuclear periphery. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by genome tiling array

Platform:

GPL7715

25 Samples

Download data: CEL, TXT

(Submitter supplied) Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel zinc-binding motif that is conserved among dicers in yeast. Although the C-terminal domain of Dcr1 still binds nucleic acids, this property is dispensable for proper functioning of Dcr1. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array

Platform:

GPL10187

12 Samples

Download data: CEL

(Submitter supplied) Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel zinc-binding motif that is conserved among dicers in yeast. Although the C-terminal domain of Dcr1 still binds nucleic acids, this property is dispensable for proper functioning of Dcr1. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9453

4 Samples

Download data

(Submitter supplied) RNA interference is involved in silencing of transposable and repetitive elements. How these elements are initially recognized by RNAi is a fundamental and unanswered question. We previously identified a class of Dicer-independent small RNAs, called primal small RNAs (priRNAs), in fission yeast. The mechanism by which Dicer-independent small RNAs are generated is not clear for any species. Here we reconstitute priRNA biogenesis in vitro and demonstrate that priRNAs can nucleate RNAi in vivo. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9453

13 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Schizosaccharomyces pombe; Schizosaccharomyces pombe 972h-

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL7715 GPL18187

10 Samples

Download data: CEL, TXT

(Submitter supplied) 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. more...

Organism:

Schizosaccharomyces pombe 972h-

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18187

1 Sample

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Schizosaccharomyces pombe; Schizosaccharomyces pombe 972h-

Type:

Expression profiling by genome tiling array

Platform:

GPL7715

9 Samples

Download data: BAR, CEL

(Submitter supplied) Expression profiling in clr4 null cells versus wild-type cells. Keywords: Expression

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2558

2 Samples

Download data

(Submitter supplied) ChIP-on-chip analyses of heterochromatin and RNAi components in fission yeast. Keywords: ChIP-on-chip

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2558

18 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7715

29 Samples

Download data: CEL, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL7715 GPL13988

24 Samples

Download data: CEL, WIG

(Submitter supplied) Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13988

8 Samples

Download data: TAB, WIG

(Submitter supplied) Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array

Platform:

GPL7715

16 Samples

Download data: CEL, TAB

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Schizosaccharomyces pombe; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by array

4 related Platforms

17 Samples

Download data: SGR, TXT

(Submitter supplied) RNAi is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by array

Platform:

GPL6503

8 Samples

Download data: TXT

(Submitter supplied) RNAi is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. more...

Organism:

Schizosaccharomyces pombe; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13304 GPL15167 GPL16192

9 Samples

Download data: SGR

(Submitter supplied) CRAC analysis was performed to identify transcripts associated with the Mkt1 protein in Schizosaccharomyces pombe

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL22682

4 Samples

Download data: BEDGRAPH, GTF

(Submitter supplied) RNA-seq was performed to identify transcripts differentially expressed in Schizosaccharomyces pombe cells lacking Mkt1.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22682

6 Samples

Download data: TXT

(Submitter supplied) The assembly of fission yeast pericentromeric heterochromatin and generation of small interfering RNAs (siRNAs) from noncoding centromeric transcripts are mutually dependent processes. How this interdependent positive feedback loop is first triggered is a fundamental unanswered question. Here we show that two distinct Argonaute (Ago1)-dependent pathways mediate small RNA generation. RNA-dependent RNA polymerase complex (RDRC) and Dicer act on specific noncoding RNAs to generate siRNAs by a mechanism that requires the slicer activity of Ago1 but is independent of pre-existing heterochromatin. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9854

13 Samples

Download data: TXT