GEO DataSets

(Submitter supplied) (1) Background: Quiescent cells have stopped dividing and show strongly reduced levels of gene expression during dormancy. In response to appropriate signals the cells can wake up and start growing again. Many histone modifications are regulated in quiescence, but their exact functions remain to be determined. (2) Methods: Here we map the different histone modifications: H3K4me3, H3K9ac, H3K9me2, H3K9me3, and the histone variant H2A.Z, comparing vegetative and quiescent fission yeast (S. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30658

50 Samples

Download data: CSV, TXT

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

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16192 GPL17225

12 Samples

Download data: BW

(Submitter supplied) Genomes pervasively produce long non-coding RNAs (lncRNAs) of largely unknown functions. Some of these lncRNAs have been implicated in roles related to ageing and associated diseases. Here we characterize aal1 (ageing-associated lncRNA 1) which is induced in non-dividing, ageing cells of fission yeast. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression of aal1 from a plasmid prolongs their lifespan, indicating that this lncRNA acts in trans. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL16192

6 Samples

Download data: BW, XLSX

(Submitter supplied) Genomes pervasively produce long non-coding RNAs (lncRNAs) of largely unknown functions. Some of these lncRNAs have been implicated in roles related to ageing and associated diseases. Here we characterize aal1 (ageing-associated lncRNA 1) which is induced in non-dividing, ageing cells of fission yeast. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression of aal1 from a plasmid prolongs their lifespan, indicating that this lncRNA acts in trans. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17225

6 Samples

Download data: XLSX

(Submitter supplied) Expression of a typical yeast gene results in ~50 3’ mRNA isoforms that are distinguished by the locations of poly(A) sites within the 3’ untranslated regions (3’ UTRs).The location of poly(A) sites with respect to the translational termination codon varies considerably among genes, but it is unknown whether this has any functional significance.Using hierarchical clustering of 3’ UTRs, we identify eight classes ofS. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL20584

2 Samples

Download data: TXT

(Submitter supplied) While nuclear pore proteins mediate nucleo-cytoplasmic transport, they can have important roles in other activities such as transcription, chromatin organization, and cell cycle regulation. The fission yeast nuclear pore protein nup211 localizes to the nuclear basket and is essential for cell viability. Nup211 is important for RNA quality control and the nuclear export of polyadenylated RNAs. Interestingly, several nup211 orthologs have also been shown to regulate transcription at the chromatin level. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

6 Samples

Download data: CSV

(Submitter supplied) RNA polymerase II (Pol II) termination is a crucial step in the transcriptional cycle, ensuring the recycling of Pol II and preventing interference with neighbouring gene transcription. Xrn2 is an enzyme with 5'-3'- exonuclease activity, responsible for degrading RNA that is still being transcribed by Pol II after cleavage at the poly(A) site, ultimately leading to Pol II termination. We have confirmed that Xrn2's catalytic activity is essential for timely transcription termination. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20584

16 Samples

Download data: BW

(Submitter supplied) RNA polymerase II (Pol II) termination is a crucial step in the transcriptional cycle, ensuring the recycling of Pol II and preventing interference with neighboring gene transcription. Xrn2 is an enzyme with 5'-3'- exonuclease activity, responsible for degrading RNA that is still being transcribed by Pol II after cleavage at the poly(A) site, ultimately leading to Pol II termination. We have confirmed that Xrn2's catalytic activity is essential for timely transcription termination. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL20584

12 Samples

Download data: BW

(Submitter supplied) ChIP-chip analyses of lysine-9 trimethylated histone H3 in clr3-CDx2 and wild type cells. Chromodomain-mediated HDAC loading sustains self-templated propagation of extended heterochromatin domain.

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6503

4 Samples

Download data: TXT

(Submitter supplied) ChIP-chip analyses of pulse-expressed H3-T7 in clr3-CDx2 and wild type cells Chromodomain-mediated HDAC loading suppresses histone turnover at self-templated heterochromatin domain. Chromodomain-mediated loading targets Clr3-CDx2 to heterochromatin domains.

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6503

4 Samples

Download data: TXT

(Submitter supplied) SUMOylation, a protein post-translational modification present in all eukaryotes, involves the covalent attachment of SUMO (small ubiquitin-like modifier) to target proteins, modulating their function, localization or stability. One of the least understood features of SUMOylation is formation of polymeric chains and their impact on DNA metabolism. Here, using Schizosaccharomyces pombe,we demonstrated that cells devoid of SUMO chains exhibit elevated spontaneous replication stress and DNA damage. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34885

6 Samples

Download data: BIGWIG, BW, NARROWPEAK

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

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL28961

356 Samples

Download data: BW

(Submitter supplied) Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyces pombe, one-third of TFs are solely homology-predicted, with few experimentally validated. We created a comprehensive library of 89 endogenously tagged S. pombe TFs, mapping their protein and chromatin interactions using immunoprecipitation mass-spectrometry and chromatin immunoprecipitation sequencing. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

12 Samples

Download data: CSV

(Submitter supplied) Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyces pombe, one-third of TFs are solely homology-predicted, with few experimentally validated. We created a comprehensive library of 89 endogenously tagged S. pombe TFs, mapping their protein and chromatin interactions using immunoprecipitation mass-spectrometry and chromatin immunoprecipitation sequencing. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28961

344 Samples

Download data: BW

(Submitter supplied) Heterochromatin enforces transcriptional gene silencing and can be epigenetically inherited, but the underlying mechanism has remained unclear.Here we show that histone deacetylation, a conserved feature of heterochromatin domains, blocks SWI/SNF subfamily remodelers involved in chromatin unraveling, thereby stabilizing modified nucleosomes that preserve gene silencing. Histone hyperacetylation, resulting from either the loss of a histone deacetylase (HDAC) or the direct targeting of histone acetyltransferase to heterochromatin, permits remodeler access, leading to silencing defects.The requirement for HDAC in heterochromatin silencing can be bypassedby impeding SWI/SNF activity. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16192 GPL20584

59 Samples

Download data: BEDGRAPH

(Submitter supplied) The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (Claspin in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. more...

Organism:

Mus musculus; Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL30172 GPL20584 GPL30658

122 Samples

Download data: BW

(Submitter supplied) The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (Claspin in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. more...

Organism:

Mus musculus; Schizosaccharomyces pombe

Type:

Other

Platforms:

GPL30658 GPL30172

70 Samples

Download data: BED, BW

(Submitter supplied) The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (Claspin in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL20584 GPL30658

52 Samples

Download data: BW, GFF3, TXT

(Submitter supplied) Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel relatively large distances from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL20584

8 Samples

Download data: BW

(Submitter supplied) Polyploidy has been implicated in genome instability and tumorigenesis. We use Schizosaccharomyces pombe diploids as a model for studying the consequences of whole genome duplications on genome integrity. In this study, our aim is to investigate the transcriptional profile between haploid and diploid S. pombe in unperturbed and MMS treated conditions (0.0075% MMS, 4 hours @ 32 degrees Celsius in YES media).

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

12 Samples

Download data: TXT