GEO DataSets

(Submitter supplied) Long non-coding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe, that heterochromatin is lost at transcribed regions in absence of RNA degradation, although establishment is not affected. more...

Organism:

Schizosaccharomyces pombe

Type:

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

Platforms:

GPL22681 GPL9453

70 Samples

Download data: TDF

(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 high throughput sequencing

Platforms:

GPL9453 GPL15167 GPL13988

10 Samples

Download data: BED

(Submitter supplied) In Schizosaccharomyces pombe, Abp1 is homologous to mammalian CENP-B. Abp1 has various seemingly independent functions in the yeast nucleus. It binds to pericentromeric repeats and contribute to heterochromatin formation (ref). Abp1 is involved in regulating the directionality of mating-type switching by regulating the transcription of a member of the recombination-promoting complex (refs). Abp1 also preserves genome integrity by silencing the Tf2 retrotransposons and protecting replication forks during pausing (ref). more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9453

4 Samples

Download data: BED

(Submitter supplied) Genome/chromosome organization is highly ordered and controls nuclear events. Here, we show that the TATA box-binding protein (TBP) interacts with the Cnd2 kleisin subunit of condensin to mediate interphase and mitotic chromosome organization in fission yeast. TBP recruits condensin onto RNA polymerase III-transcribed (Pol III) genes and highly transcribed Pol II genes; condensin in turn associates these genes with centromeres. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9453 GPL13988

13 Samples

Download data: WIG

(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) Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. more...

Organism:

Homo sapiens; Arabidopsis thaliana; Drosophila melanogaster; Xenopus laevis; Mus musculus; Schizosaccharomyces pombe; Danio rerio; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

13 related Platforms

64 Samples

Download data: TXT

(Submitter supplied) Homeostatic control mechanisms are essentil to life. One such mechanism, the unfolded protein response (UPR) operates in all eukarytic cells to adjust protein folding capacity of the endoplasmic reticulum (ER) according to need. UPR induction in all eurkarytic cells to date involves Ire1 (kinase/endonuclease transmembrane protein) mediated a non-convential splicing of Hac1/XBP1 mRNA, encoding for a potent transcription factor. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9453 GPL13988

15 Samples

Download data: WIG

(Submitter supplied) We report the development of a novel strand-specific ChIP-seq strategy and application of this strategy in studying genome instability events

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9453

66 Samples

Download data: BED

(Submitter supplied) We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher-resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, ~152 bp, in fission yeast and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstream nucleosomes. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9453

4 Samples

Download data: BOWTIE

(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) 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) We provide evidence of the generation of Rdp1-mediated secondary siRNAs in vivo in fission yeast. Secondly, we show that the presence of Ago1-associated siRNAs does not guarantee robust silencing.

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9854 GPL9453

3 Samples

Download data: BEDGRAPH, FNA, GFF