GEO DataSets

(Submitter supplied) The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which requires a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. more...

Organism:

Saccharomyces cerevisiae S288C

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33992

6 Samples

Download data: FA, WIG

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

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

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

Platforms:

GPL33992 GPL31112

14 Samples

Download data: WIG

(Submitter supplied) The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which requires a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31112

8 Samples

Download data: FA, WIG

(Submitter supplied) The MYST HAT Sas2 is part of the SAS-I complex. The target for acetylation by Sas2 is Lys16 of histone H4 (H4 K16Ac). This acetylation site marks euchromatic regions and opposes the spreading of heterochromatin at telomere-proximal regions. Changes of SAS-I-mediated H4 K16Ac on a genome-wide scale comparing wt and sas2∆ cells were investigated in this study. We found a pronounced, genome-wide loss of H4 K16 acetylation in the body of transcribed genes in the absence of Sas2. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

4 Samples

Download data: CEL, TXT

(Submitter supplied) H2A.Z is a highly conserved histone variant involved in several key nuclear processes. It is incorporated into promoters by SWR-C-related chromatin remodeling complexes, but whether it is also actively excluded from non-promoter regions is not clear. Here, we provide genomic and biochemical evidence that RNA polymerase II (RNAPII) elongation-associated histone chaperones FACT and Spt6 both contribute to restricting H2A.Z from intragenic regions. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL18340 GPL4131

116 Samples

Download data: GPR

(Submitter supplied) Histone chaperones are an important class of factors that regulate chromatin accessibility for DNA-templated processes. Spt6 is a conserved histone chaperone and key regulator of transcription and chromatin structure. However, its functions outside of these roles have been little explored. In this work, we demonstrate a role for Spt6 in DNA replication and more broadly as a regulator of genome stability. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

22 Samples

Download data: BW

(Submitter supplied) Spt6 is a conserved factor that controls transcription and chromatin structure across the genome. Although viewed as an elongation factor, spt6 mutations allow transcription from within coding regions, suggesting that Spt6 also controls initiation. To comprehensively characterize the requirement for Spt6 in transcription, we have used four approaches: TSS-seq and TFIIB ChIP-nexus to assay transcription initiation, NET-seq to assay elongating RNAPII, and MNase-seq to assay nucleosome occupancy and positioning. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL13821 GPL19756 GPL17143

21 Samples

Download data: BW

(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

Platform:

GPL13821

14 Samples

Download data: BW, TXT

(Submitter supplied) CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

8 Samples

Download data: BW

(Submitter supplied) CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

6 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL18340 GPL24876 GPL17342

316 Samples

Download data: BIGWIG, GPR

(Submitter supplied) The genetic information encoded in DNA is framed by additional layers of information, referred to as the epigenome. Epigenetic marks such as DNA methylation, histone modifications and histone variants are concentrated on specific genomic sites as means to instruct, but also sometimes as a consequence of, gene expression. How this information is maintained, notably in the face of transcription, is not understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

36 Samples

Download data: BIGWIG

(Submitter supplied) The genetic information encoded in DNA is framed by additional layers of information, referred to as the epigenome. Epigenetic marks such as DNA methylation, histone modifications and histone variants are concentrated on specific genomic sites as means to instruct, but also sometimes as a consequence of, gene expression. How this information is maintained, notably in the face of transcription, is not understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL18340 GPL24876

280 Samples

Download data: BED, GPR, XLSX

(Submitter supplied) Strain background is Saccharomyces cerevisiae wzy42 histone mutant strain with pWZ403 Myc-HHT2-HHF2 plasmid and pGAL1/10 FLAG-HHT1-HHF1 integrated gene. Cells were grown in YP+2% raffinose until mid-log (OD600=0.5) and arrested with alpha factor. When most of Cells were in G1 phase, added galactose (final conc. 2%) and harvested cells after 1 hour. Fixed cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

40 Samples

Download data: BIGWIG, WIG

(Submitter supplied) Spt6 is an essential histone chaperone that mediates nucleosome reassembly during gene transcription. Spt6 interacts with elongating RNA polymerase II (RNAPII) via a tandem Src2 homology (tSH2) domain, but it is not known whether this particular interaction is required for the nucleosome reassembly activity of Spt6. Here, we show that Spt6 recruitment to genes and its nucleosome reassembly functions are largely independent of association with RNAPII. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL17342

12 Samples

Download data: BW, TXT

(Submitter supplied) Asf1, through its histone chaperone activity, helps chromatin closing/opening during DNA replication, repair, recombination and transcription. Despite extensive research on Asf1-mediated physiological functions, a genome-wide localization map is lacking, limiting our knowledge of chromosomal features targeted by Asf1. We present a high-resolution genome-wide map of Asf1, localizing at essentially all pol III-transcribed genes, highly active pol II-transcribed genes and heterochromatic features. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

3 Samples

Download data: BEDGRAPH

(Submitter supplied) The FACT complex and Spt6 are conserved histone chaperones that are recruited to the open reading frames of transcribed genes. In this study, we provide evidence that FACT interaction with acetylated H3 tail is important for its localization to the coding sequences. Pol II CTD kinase Kin28 additionally stimulates FACT recruitment to a subset of genes. Pol II occupancies in the 5’ ends of transcribed genes are greatly reduced on depleting FACT, whereas reduced occupancies at the 3’ ends were observed upon Spt6 depletion indicating that these factors modulate Pol II progression through distinct regions of transcribed coding sequences. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10930

28 Samples

Download data: TXT

(Submitter supplied) A two-colour cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. We describe a fluorescent reporter system that exploits the functional genomic tools available in budding yeast to systematically assess consequences of genetic perturbations on gene expression. We used our Reporter-Synthetic Genetic Array (R-SGA) method to screen for regulators of core histone gene expression. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7070

5 Samples

Download data: BAR, CEL

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL9377 GPL7070

185 Samples

Download data: BAR, CEL, WIG

(Submitter supplied) Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

16 Samples

Download data: WIG