GEO DataSets

(Submitter supplied) The S. cerevisiae Forkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering. As stimulators of early origin activation, we hypothesized that Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide. Existing methods, however, were not well suited to quantitative, genome-wide measurements of origin firing between strains and conditions. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

64 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL19756 GPL14887

70 Samples

Download data: PAIR

(Submitter supplied) The S. cerevisiae Forkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering. As stimulators of early origin activation, we hypothesized that Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide. Existing methods, however, were not well suited to quantitative, genome-wide measurements of origin firing between strains and conditions. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL14887

6 Samples

Download data: PAIR

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

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array; Other

Platforms:

GPL14887 GPL13821

28 Samples

Download data: BED, PAIR, WIG

(Submitter supplied) Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

22 Samples

Download data: BED

(Submitter supplied) Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14887

6 Samples

Download data: PAIR, WIG

(Submitter supplied) Forkhead box (FOX) transcription factors regulate a wide variety of cellular functions in higher eukaryotes, including cell cycle control and developmental regulation. In Saccharomyces cerevisiae, Forkhead proteins Fkh1 and Fkh2 perform analogous functions, regulating genes involved in cell cycle control, while also regulating matingtype silencing and switching involved in gamete development. Recently, we revealed a novel role for Fkh1 and Fkh2 in the regulation of replication origin initiation timing, which, like donor preference in mating-type switching, appears to involve long-range chromosomal interactions, suggesting roles for Fkh1 and Fkh2 in chromatin architecture and organization. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14887

30 Samples

Download data: PAIR

(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; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL9377 GPL14887

56 Samples

Download data: PAIR

(Submitter supplied) The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function. The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure. Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array; Other

Platform:

GPL14887

30 Samples

Download data: PAIR

(Submitter supplied) The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function. The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure. Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL9377

26 Samples

Download data: TXT

(Submitter supplied) The replication of eukaryotic genomes is highly regulated to ensure faithful transmission of all genetic information through cell divisions. In addition to stringent control of origin initiation by cell cycle controls and DNA damage checkpoints, spatial and temporal control of origins serves to stage and balance replication of different genomic regions, with potential implications for development and genome stability. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL27812

48 Samples

Download data: BED

(Submitter supplied) Initiation of eukaryotic chromosome replication follows a spatiotemporal program. Current model suggests that replication origins compete for a limited pool of initiation factors. However, it remains to be answered how these limiting factors are preferentially recruited to early origins. Here, we report that Dbf4 is enriched at early origins through its interaction with forkhead transcription factors Fkh1 and Fkh2. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL13821 GPL21656

13 Samples

Download data: BIGWIG

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

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL14887 GPL13821

34 Samples

Download data: PAIR

(Submitter supplied) Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

4 Samples

Download data: TXT

(Submitter supplied) Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL14887

30 Samples

Download data: PAIR

(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) Fourteen yeast mutants with an extended S-phase were identified by a novel genome-wide screen. These mutants are associated with the DNA replication machinery, cell-cycle control and dNTP synthesis. We determined the genome-wide DNA replication timing profile of all these mutants as well as wild type, by FACS-sorting G1- and S-phase cells and co-hybridizing their DNA to Agilent genomic tiling arrays, in four repeats each. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4131

58 Samples

Download data: SRR, TXT

(Submitter supplied) Sequencing of mononucleosomal DNA during G1 and S phases in Saccharomyces cerevisiae

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

4 Samples

Download data: WIG

(Submitter supplied) The occupancy states of DNA-binding nucleosomes and subnucleosome-sized proteins (e.g.  transcription factors, replication proteins, etc.) determine the chromatin accessibility landscape and provide additional regulatory context for DNA-templated processes including transcription and DNA replication. Throughout the mitotic cell division cycles, the transcriptome undergoes periodic reprogramming along with replication- and mitosis-induced global chromatin reconfiguration; however, profiling of the cell cycle-specific chromatin dynamics and understandings of its regulatory mechanisms remain limited. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL19756

59 Samples

Download data: CSV

(Submitter supplied) This study defines nucleosome occupancy as a novel parameter for regulating origin activities. Nucleosome occupancy at origins was assessed using histone H3 ChIP-seq during G1 and G2M. Origin activity was determined using BrdU ChIP-seq.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

37 Samples

Download data: SGR