Similar studies for GEO DataSets (Select 200060181) - GEO DataSets

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Items: 20

Select item 2000601811.

Threonine-4 of the budding yeast RNAP II CTD couples transcription with Htz1-mediated chromatin remodeling

(Submitter supplied) The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAP II) consists of repeated YSPTSPS heptapeptides and connects transcription with cotranscriptional events. Threonine-4 (Thr4) of the CTD repeats has been shown to function in histone mRNA 3'-end processing in chicken cells and in transcriptional elongation in human cells. Here, we demonstrate that, in budding yeast, Thr4, although dispensable for growth in rich media, is essential in phosphate-depleted or galactose-containing media. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13272
4 Samples

Download data: TXT

Series

Accession:: GSE60181

ID:: 200060181

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000954192.

RNA Pol II CTD mutants

(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

Platforms:: GPL22008 GPL22009
8 Samples

Download data: FTR, GFF

Series

Accession:: GSE95419

ID:: 200095419

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000954183.

ChIP-chip in RNA Pol II mutants

(Submitter supplied) The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific “readers.” While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. more...

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by genome tiling array

Platforms:: GPL22008 GPL22009
5 Samples

Download data: FTR, GFF

Series

Accession:: GSE95418

ID:: 200095418

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000954174.

RNA expression analysis in RNA Pol II CTD mutants

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by genome tiling array

Platform:: GPL22009
3 Samples

Download data: FTR, GFF

Series

Accession:: GSE95417

ID:: 200095417

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000239605.

Budding yeast RNA polymerase II CTD phosphorylation and transcription termination factor localization

(Submitter supplied) Whole genome analysis of total RNA pol II, Ser2-, Ser5- and Ser7-phosphorylated RNA pol II, in WT and mutants of the C-terminal domain (CTD) kinases Ctk1 and Kin28, and localization of the termination factors Pcf11, Nrd1 and Rat1.

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by genome tiling array

Platform:: GPL4613
12 Samples

Download data: GFF, PAIR, TXT

Series

Accession:: GSE23960

ID:: 200023960

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000375196.

Threonine-4 of Mammalian RNA Polymerase II CTD is Targeted by Polo-like Kinase-3 and Required for Transcriptional Elongation

(Submitter supplied) Eukaryotic RNA polymerase II (Pol II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of the large subunit (Rpb1). Differential phosphorylation of Ser2, Ser5, and Ser7 in the 5’ and 3’ regions of genes coordinates the binding of transcription and RNA processing factors to the initiating and elongating polymerase complexes. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9052
9 Samples

Download data: BED, WIG

Series

Accession:: GSE37519

ID:: 200037519

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000257227.

Chip-chip from wt and ino80 mutant cells with Htz1

(Submitter supplied) Global regulation of H2A.Z localization by the INO80 chromatin remodeling enzyme is essential for genome integrity. Chromatin immunoprecipitation (ChIP) of Htz1 in wild-type and ino80 mutant yeast demonstrated that Ino80 plays a role in replacing Htz1 with H2A.

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by genome tiling array

Platform:: GPL2625
8 Samples

Download data: GPR

Series

Accession:: GSE25722

ID:: 200025722

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000978278.

RNA pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD phosphorylation and transcriptional direction

(Submitter supplied) Using pol II mutants in human cells we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; H3K36me3 shifted within genes toward 5’ ends and H3K4me2 extended further upstream of start sites. Slow transcription also evoked a hyperphosphorylation of CTD Ser2 residues at 5’ ends of genes that is conserved in yeast. We propose a “dwell-time in the target zone” model to explain the effects of transcriptional dynamics on establishment of co-transcriptionally deposited protein modifications. more...

Organism:: Saccharomyces cerevisiae; Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms
53 Samples

Download data: BW, TDF

Series

Accession:: GSE97827

ID:: 200097827

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001071669.

Chromatin immunoprecipitation and expression analysis in WT and hrr25 mutant cells

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

Organism:: Saccharomyces cerevisiae

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

Platforms:: GPL17342 GPL22008
30 Samples

Download data: FTR, GFF

Series

Accession:: GSE107166

ID:: 200107166

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20010716510.

RNA-seq of WT, hrr25as, and hrr25is treated with inhibitors

(Submitter supplied) The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcrption. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific "readers." While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17342
16 Samples

Download data: CSV

Series

Accession:: GSE107165

ID:: 200107165

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010716411.

ChIP-chip in Hrr25 mutant strains

(Submitter supplied) The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcrption. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific readers. While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. more...

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by genome tiling array

Platform:: GPL22008
14 Samples

Download data: FTR, GFF

Series

Accession:: GSE107164

ID:: 200107164

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20009741612.

The histone variant H2A.Z promotes efficient co-transcriptional splicing in S. cerevisiae

(Submitter supplied) In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from pre-messenger RNA (pre-mRNA). Recent studies show the process of RNA-synthesis and RNA-processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In S. cerevisiae, H2A.Z is deposited into chromatin by the SWR1-complex, is found near the 5’ ends of protein-coding genes, and has been implicated in transcription regulation. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13821
15 Samples

Download data: XLSX

Series

Accession:: GSE97416

ID:: 200097416

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014227313.

Chromatin Remodeler Ino80C acts independently of H2A.Z to evict promoter nucleosomes and stimulate transcription of highly expressed genes in yeast

(Submitter supplied) The chromatin remodelers (CRs) SWI/SNF and RSC function in evicting promoter nucleosomes at highly expressed yeast genes, particularly those activated by transcription factor Gcn4. Ino80 remodeling complex (Ino80C) can establish nucleosome-depleted regions (NDRs) in reconstituted chromatin, and was implicated in removing histone variant H2A.Z from the -1 and +1 nucleosomes flanking NDRs; however, Ino80C’s function in transcriptional activation in vivo is not well understood. more...

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL23014
101 Samples

Download data: BW

Series

Accession:: GSE142273

ID:: 200142273

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006171314.

HDACs and Phosphorylated Pol II CTD recruit Spt6 for cotranscriptional histone reassembly

(Submitter supplied) Spt6 is a multifunctional histone chaperone involved in the maintenance of chromatin structure during elongation by RNA polymerase II (Pol II). Spt6 has a tandem SH2 (tSH2) domain within its C-terminus that recognizes Pol II CTD peptides phosphorylated on Ser2, Ser5 or Try1 in vitro. Deleting the tSH2 domain, however, only has a partial effect on Spt6 occupancy in vivo, suggesting that more complex mechanisms are involved in the Spt6 recruitment. more...

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by genome tiling array; Expression profiling by RT-PCR

Platform:: GPL18340
28 Samples

Download data: BED, GPR

Series

Accession:: GSE61713

ID:: 200061713

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20006818115.

Rtr1 regulates global levels of RNA Polymerase II CTD phosphorylation during transcription elongation

(Submitter supplied) RNA Polymerase Serine 5 phosphorylation (H14 antibody) is examined in wt and rtr1 deletion conditions to see if deletion of rtr1 causes a redistribution of these marks across open reading frames.

Organism:: Saccharomyces cerevisiae

Type:: Genome binding/occupancy profiling by genome tiling array

Platform:: GPL4130
8 Samples

Download data: TXT

Series

Accession:: GSE68181

ID:: 200068181

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20008342616.

Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast

(Submitter supplied) Eukaryotic gene expression requires that RNA Polymerase II (RNAP II) gain access to DNA in the context of chromatin. The C-terminal domain (CTD) of RNAP II recruits chromatin modifying enzymes to promoters, allowing for transcription initiation or repression. Specific CTD phosphorylation marks facilitate recruitment of chromatin modifiers, transcriptional regulators, and RNA processing factors during the transcription cycle. more...

Organism:: Schizosaccharomyces pombe

Type:: Expression profiling by array

Platform:: GPL21587
16 Samples

Download data: GPR

Series

Accession:: GSE83426

ID:: 200083426

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20000557217.

H3K4me3 ChIP chips

(Submitter supplied) In yeast and other eukaryotes, the histone methyltransferase Set1 mediates methylation of lysine 4 on histone H3 (H3K4me). This modification marks the 5' end of transcribed genes in a 5' to 3' tri- to di- to monomethyl gradient, and promotes association of chromatin remodeling enzymes that regulate transcription. In a screen to identify factors that control the distinct H3K4 methylation states, we identified Ctk1, the serine 2 C-terminal domain (CTD) kinase for RNA polymerase II (RNAP II). more...