GEO DataSets

(Submitter supplied) RNA-Seq analysis of S. cerevisiae to study the biology of centromere and pericentromere transcripts.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

4 Samples

Download data: TXT

(Submitter supplied) Kinetochores assemble on centromeres via histone H3 variant CENP-A and low levels of noncoding centromere transcripts (cenRNAs). The latter are ensured by downregulation of RNA polymerase II (RNAPII) and turnover by the nuclear exosome. Using S. cerevisiae, we now add kinase Rio1 to this scheme. Yeast cenRNAs are produced in very low amounts either as short (median lengths of 231nt) or long (4,458nt) transcripts, in a 1:1 ratio. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

6 Samples

Download data: TXT

(Submitter supplied) Centromeres are the regions of eukaryotic chromosomes where kinetochores are assembled and direct the correct segregation of chromosomes. Active centromeres are defined by presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location CENP-A chromatin and the kinetochore is maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23689 GPL25575

15 Samples

Download data: BW

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

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23689 GPL17225 GPL25575

59 Samples

Download data: BW

(Submitter supplied) Centromeres are the regions of eukaryotic chromosomes where kinetochores are assembled and direct the correct segregation of chromosomes. Active centromeres are defined by presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location CENP-A chromatin and the kinetochore is maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

40 Samples

Download data: BW

(Submitter supplied) Centromeres are the regions of eukaryotic chromosomes where kinetochores are assembled and direct the correct segregation of chromosomes. Active centromeres are defined by presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location CENP-A chromatin and the kinetochore is maintained at that location though a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

4 Samples

Download data: BW

(Submitter supplied) Paired-end sequencing study of nucleosomal DNA prepared from budding yeast by micrococcal nuclease digestion.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

4 Samples

Download data: TXT

(Submitter supplied) Specialized chromatin containing CENP-A nucleosomes instead of H3 nucleosomes is found at all centromeres. However, the mechanisms that specify the locations at which CENP-A chromatin is assembled remain elusive in organisms with regional, epigenetically regulated centromeres. It is known that normal centromeric DNA is transcribed in several systems including the fission yeast, Schizosaccharomyces pombe. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7715

24 Samples

Download data: BAR, CEL

(Submitter supplied) Accurate chromosome segregation requires centromeres (CENs), the chromosomal sites where kinetochores form, to bridge DNA and attach to microtubules. In contrast to most eukaryotes, Saccharomyces cerevisiae possesses sequence-defined point centromeres. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) of four kinetochore components reveals regions of overlapping, extra-centromeric protein localization upon overproduction of the centromeric histone, Cse4 (CENP-A or CenH3). more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

13 Samples

Download data: BED, SGR, TXT

(Submitter supplied) Centromere is the chromosomal locus at which kinetochore is assembled to direct chromosome segregation. Histone H3 variant CENP-A epigenetically marks active centromeres; however, the mechanism by which CENP-A propagates at the centromere, replacing histone H3, remains poorly understood. Using fission yeast, we find that CENP-ACnp1 chromatin assembly at the centromere requires the Ino80 ATP-dependent chromatin remodeling complex which removes histone H3-containing nucleosomes from associated chromatin. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

98 Samples

Download data

(Submitter supplied) Accurate chromosome segregation requires that sister kinetochores biorient and attach to microtubules from opposite poles. Kinetochore biorientation relies on the underlying centromeric chromatin, which provides a platform to assemble the kinetochore and to recruit the regulatory factors that ensure the high fidelity of this process. To identify the centromeric chromatin determinants that contribute to chromosome segregation, we performed two complementary unbiased genetic screens using a library of mutants in every residue of histone H3 and H4. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

22 Samples

Download data: TXT

(Submitter supplied) Precise localization of the histone H3 variant CENP-A(Cse4) to centromeres is essential for accurate chromosome segregation. In budding yeast, CENP-A(Cse4) is regulated by ubiquitin-mediated proteolysis to ensure its exclusive localization to the centromere. Overexpression of CENP-A(Cse4) is lethal when the CENP-A(Cse4) E3 ubiquitin ligase, Psh1, is deleted. CENP-A(Cse4) mislocalizes to promoters in this condition, so we investigated if there was an effect on gene expression of downstream genes using RNA-seq.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

34 Samples

Download data: TXT, XLSX

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL13821 GPL17342

42 Samples

Download data: BED, WIG

(Submitter supplied) Precise localization of the histone H3 variant CENP-A(Cse4) to centromeres is essential for accurate chromosome segregation. In budding yeast, CENP-A(Cse4) is regulated by ubiquitin-mediated proteolysis to ensure its exclusive localization to the centromere. Overexpression of CENP-A(Cse4) is lethal when the CENP-A(Cse4) E3 ubiquitin ligase, Psh1, is deleted. To identify the genomic sites of CENP-A(Cse4) mislocalization in this condition, we investigated the genome-wide mislocalization pattern of CENP-A(Cse4) by ChIP-seq.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

8 Samples

Download data: BED, WIG

(Submitter supplied) The segregation of maternal centromeres away from the paternal ones during the first division of meiosis depends on the attachment of sister kinetochores to microtubules emanating from the same spindle pole. In budding yeast monopolar attachment requires the recruitment to kinetochores of a protein complex called monopolin. The biochemical function of monopolin was unknown. Here, we have identified the casein kinase I Hrr25 as a hitherto unknown subunit of monopolin. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL347

5 Samples

Download data: CEL

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

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL7715 GPL13988

5 Samples

Download data: BAR, BED, CEL, WIG

(Submitter supplied) At Schizosaccharomyces pombe centromeres, heterochromatin formation is required for de novo incorporation of the histone H3 variant CENP-A/Cnp1, which in turn directs kinetochore assembly and ultimately chromosome segregation during mitosis. Noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (Pol II) directs heterochromatin formation via the RNAi machinery, but also through RNAiindependent RNA processing factors. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13988

3 Samples

Download data: BED, WIG

(Submitter supplied) At Schizosaccharomyces pombe centromeres, non-coding RNAs are transcribed by RNA polymerase II and processed by the RNAi machinery to direct heterochromatin formation. Mediator is a regulator of RNA polymerase II transcription and we here demonstrated that it also controls the levels of centromeric transcripts. Loss of the Mediator subunit Med20 increases transcription of non-coding RNAs and disrupts the centromeric heterochromatin structure. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array

Platform:

GPL7715

2 Samples

Download data: BAR, CEL

(Submitter supplied) Centromeres are the chromosomal loci essential for faithful chromosome segregation during cell division. Although centromeres are transcribed and produce non-coding RNAs (cenRNAs) that affect centromere function, we still lack a mechanistic understanding of how centromere transcription is regulated. Here, using a targeted RNA isoform sequencing approach, we identified the transcriptional landscape at and surrounding all centromeres in budding yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30973

16 Samples

Download data: BAM, BW, TSV

(Submitter supplied) In order to take an unbiased approach and discover all the locations of Cse4 in the genome, we utilized formaldehyde crosslinking and immunoprecipitation followed by hybridization to DNA microarrays. We analyzed the location of Cse4 in three different strains; one in which the endogenous Cse4 is tagged with 12Myc epitopes (Cse4-12Myc), and one which contained both the endogenous Cse4 (untagged) and an ectopic copy of Cse4-12Myc expressed from the GAL1-10 promoter (pGAL1-10-Cse4-12Myc), and one in which Cse4 is tagged with 3HA epitopes (Cse4-3HA). more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8956

6 Samples

Download data: GPR