GEO DataSets

(Submitter supplied) Restricting the localization of the centromeric histone H3 variant CENP-A to centromeres is essential to prevent chromosomal instability (CIN). Mislocalization of overexpressed CENP-A contributes to CIN in yeast, fly, and human cells. CENP-A is overexpressed in many cancers. Therefore, defining mechanisms that prevent CENP-A mislocalization will help us understand how CENP-A overexpression contributes to CIN in cancer. more...

Organism:

Saccharomyces cerevisiae S288C

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23380

8 Samples

Download data: BEDGRAPH, NARROWPEAK

(Submitter supplied) The evolutionarily conserved F-box proteins Met30 and Cdc4 interact with Cse4 in vivo and cooperatively regulate cellular levels of Cse4 by ubiquitin-mediated proteolysis. To survey genomewide localization of Cse4 in met30-6 and cdc4-1 mutants, chromatin immunoprecipitation (ChIP) was carried out in strains expressing HA-tagged Cse4 from its endogenous promoter. Prominent Cse4 peaks were observed only at centromeres (CENs) in all three strains, and a statistically significant increase of Cse4 enrichment at CENs was observed in the mutants. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19756 GPL17342

16 Samples

Download data: BEDGRAPH, NARROWPEAK

(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:

GPL17342 GPL13821

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) 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:

GPL19756 GPL17342

27 Samples

Download data

(Submitter supplied) Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could lead to ectopic centromere formation and missegregation, and could affect DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into noncentromeric regions. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

8 Samples

Download data: TXT

(Submitter supplied) Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could lead to ectopic centromere formation and missegregation, and could affect DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into noncentromeric regions. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

19 Samples

Download data: BW

(Submitter supplied) Mislocalization of CENP-A to non-centromeric regions contributes to chromosomal instability (CIN). Here, we defined a role for the histone H3/H4 chaperone CHAF1B in preventing mislocalization of CENP-A and CIN.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: BW

(Submitter supplied) The centromeric histone H3 variant CENP-A is overexpressed in many cancers. Mislocalization of CENP-A to non-centromeric regions contributes to chromosomal instability (CIN), a hallmark of cancer. Despite these observations, pathways that promote and prevent CENP-A mislocalization remain poorly defined. Here, we performed a genome-wide RNAi screen to identify regulators of CENP-A localization. We identified DNAJC9, a J-domain protein as a lead candidate from the screen and showed that cells depleted for DNAJC9 exhibit mislocalization of CENP-A, enrichment of CENP-A in chromatin, and CIN phenotypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: BED, BIGWIG

(Submitter supplied) Cdc7 kinase is known to initiate DNA replication, but it is unknown where Cdc7 is found within the genome. We modified the Calling Cards method that uses the Ty5 retrotransposon to investigate Cdc7 binding in the genome. The Ty5 retrotransposon is inserted into the genome by DNA transcription factors or replication factors binding within the genome. We find that Cdc7 inserts Ty5 transposons throughout chromosomes and furthermore creates more Ty5 insertions into regions of DNA that are known to replicate early. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

4 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Centromeres play several important roles in ensuring proper chromosome segregation. Not only do they promote kinetochore assembly for microtubule attachment, but they also support robust sister chromatid cohesion at pericentromeres and facilitate replication of centromeric DNA early in S phase. However, it is still elusive how centromeres orchestrate all these functions at the same site. Here we show that the budding yeast Dbf4-dependent kinase (DDK) accumulates at kinetochores in telophase, facilitated by the Ctf19 kinetochore complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL16234

8 Samples

Download data: WIG

(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

(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) In eukaryotes, CDC7 kinase is crucial for DNA replication initiation and has been involved in fork processing and replication stress response. Human CDC7 requires the binding of either one of two regulatory subunits, DBF4 and DRF1, for its activity. However, it is unclear whether the two regulatory subunits target CDC7 to a specific set of substrates, thus having different biological functions, or if they act redundantly. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL10123

12 Samples

Download data: BED, TXT

(Submitter supplied) Eukaryotic genomes are replicated in spatiotemporal patterns that are stereotypical for individual genomes and developmental profiles. In the model system S. cerevisiae, two primary mechanisms determine the preferential activation of replication origins during early S phase, thereby largely defining the consequent replication profiles of these cells. Both mechanisms are thought to act through specific recruitment of a rate-limiting initiation factor, Dbf4-dependent kinase (DDK), to a subset of licensed replication origins. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26302 GPL27812

44 Samples

Download data: BED

(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) 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