GEO DataSets

(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) 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

(Submitter supplied) RNAi is a conserved mechanism in which small RNAs induce silencing of complementary targets. How Argonaute-bound small RNAs are targeted for degradation is not well understood. We show here that the adenyl-transferase Cid14, a member of the TRAMP complex, and the uridyl-transferase Cid16 add non-templated nucleotides to Argonaute-bound small RNAs in fission yeast. The tailing of Argonaute-bound small RNAs in vitro recruits the 3’-5’ exonuclease Rrp6 to degrade small RNAs. more...

Organism:

Schizosaccharomyces pombe

Type:

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

Platform:

GPL22681

30 Samples

Download data: TDF

(Submitter supplied) Small-RNA (sRNA)-guided transcriptional gene silencing by Argonaute (Ago)-containing complexes is fundamental to genome integrity and epigenetic inheritance. The RNA cleavage (“Slicer”) activity of Argonaute has been implicated in both sRNA maturation and target RNA cleavage. Typically, Argonaute slices and releases the passenger strand of duplex sRNA to generate active silencing complexes, but it remains unclear whether slicing of target nascent RNAs, or other RNAi components, also contributes to downstream transcriptional silencing. more...

Organism:

Schizosaccharomyces pombe

Type:

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

Platform:

GPL13988

10 Samples

Download data: TDF

(Submitter supplied) Ago1 can mediate transcriptional gene silencing without slicing nascent RNA target

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13988

2 Samples

Download data: TDF

(Submitter supplied) Ago1 can mediate transcriptional gene silencing without slicing nascent RNA target

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13988

2 Samples

Download data: TDF

(Submitter supplied) Ago1 can mediate transcriptional gene silencing without slicing nascent RNA target

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13988

6 Samples

Download data: TDF

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

Organism:

Schizosaccharomyces pombe

Type:

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

Platforms:

GPL6503 GPL16192

12 Samples

Download data: SGR, TXT

(Submitter supplied) Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast. Occupancy profiling of Red1, Mtl1, and Mmi1 proteins in fission yeast.

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6503

10 Samples

Download data: TXT

(Submitter supplied) Co-transcriptional RNA processing and surveillance factors mediate heterochromatin formation in fission yeast. In addition to RNAi, RNA elimination machinery including MTREC (Mtl1-Red1 core) and the exosome are involved in facultative heterochromatin assembly, however, the exact mechanisms remain unclear. Here we show that RNA elimination factors cooperate with the conserved exoribonuclease Dhp1/Rat1/Xrn2, which couples pre-mRNA 3’-end processing to transcription termination, to promote premature termination and facultative heterochromatin formation at meiotic genes. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16192

2 Samples

Download data: SGR

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

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array; Other

Platforms:

GPL13988 GPL19654

8 Samples

Download data: BEDGRAPH, BIGWIG, TXT

(Submitter supplied) Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes. In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex exosome. Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Xrn2. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL13988

5 Samples

Download data: BIGWIG