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TranscriptomicsChIP-chip by array of yeast to determine genome-wide occupancy profiles for RNA polymerase (Pol) II, its phosphorylated forms, and transcription factors
To investigate the chromatin transcription cycle, we determined genome-wide occupancy profiles for RNA polymerase (Pol) II, its phosphorylated forms, and transcription factors in growing yeast. ChIP-chip was performed to identify the genomic binding locations for Rpb3, TFIIB, Tfg1, Kin28, Cet1, Spt4...
ORGANISM(S): Saccharomyces cerevisiae 
2010-08-23 | E-TABM-1033 | biostudies-arrayexpress
TranscriptomicsStructures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue
Bypass of Ess1 (Bye1) is a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. Bye1 binds with its TFIIS-like domain (TLD) to RNA polymerase (Pol) II. Using a Bye1-TAP strain ChIP-chip was performed to examine the genome-wide association of Bye1 ...
ORGANISM(S): Saccharomyces cerevisiae 
2013-09-23 | E-MTAB-1894 | biostudies-arrayexpress
TranscriptomicsCTD tyrosine phosphorylation impairs termination factor recruitment to transcribing RNA polymerase II
ChIP-chip was performed to identify the genomic binding locations for the termination factors Nrd1, and Rtt103, and for RNA polymerase (Pol) II phosphorylated at the tyrosine 1 and threonine 4 position of its C-terminal domain (CTD). In different phases of the transcription cycle, Pol II recruits di...
ORGANISM(S): Saccharomyces cerevisiae 
2012-06-29 | E-MTAB-1060 | biostudies-arrayexpress
TranscriptomicsMolecular basis for coupling transcription termination to non-coding RNA degradation
The Nrd1-Nab3-Sen1 (NNS) complex plays a pivotal role in the control of pervasive transcription and the generation of sn- and snoRNAs in S. cerevisiae. The NNS-complex terminates transcription of non-coding RNA genes and promotes processing/degradation of transcripts by the nuclear exosome. To asses...
ORGANISM(S): Saccharomyces cerevisiae 
2014-04-24 | E-MTAB-2175 | biostudies-arrayexpress
TranscriptomicsThe repetitive C-terminal region of Spt5 recruits 3'-end processing factors in yeast
ChIP-chip was performed to identify the genomic binding locations for the termination factors RNA14 and RNA15, and for Rpb3 in wildtype and mutant backgrounds.
ORGANISM(S): Saccharomyces cerevisiae 
2012-12-15 | E-TABM-1225 | biostudies-arrayexpress
TranscriptomicsThe Nrd1 CTD-interaction domain contributes to the choice of RNA polymerase II termination pathway and couples to RNA processing by the nuclear exosome
The RNA polymerase II (RNApII) C-terminal domain (CTD)-interacting domain (CID) proteins are involved in two distinct termination pathways and recognize different phosphorylated forms of CTD. To investigate the role of differential CTDM-^VCID interactions in the choice of termination pathway, we alt...
ORGANISM(S): Saccharomyces cerevisiae 
2013-12-04 | E-MTAB-1626 | biostudies-arrayexpress
TranscriptomicsCap completion and CTD kinase recruitment govern the initiation-elongation transition of RNA polymerase II
After transcription initiation, RNA polymerase (Pol) II escapes from the promoter and recruits elongation factors. Here we used chromatin immunoprecipitation (ChIP) to elucidate the general initiation-elongation transition of Pol II in yeast. We extended our ChIP-chip occupancy profiling to capping ...
ORGANISM(S): Saccharomyces cerevisiae 
2013-07-30 | E-MTAB-1552 | biostudies-arrayexpress
TranscriptomicsRNA polymerase II termination involves CTD tyrosine dephosphorylation by CPF subunit Glc7
At the 3'-ends of genes, RNA polymerase (Pol) II is dephosphorylated at tyrosine 1 residues of its C-terminal domain (CTD), resulting in recruitment of transcription termination factors. We show that the multisubunit cleavage and polyadenylation factor (CPF) is a Pol II CTD phosphatase and its Glc7 ...
ORGANISM(S): Saccharomyces cerevisiae 
2013-12-16 | E-MTAB-1528 | biostudies-arrayexpress
TranscriptomicsReal-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection
During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging) to dissect the real-time kinetics of cellular and viral transcriptio...
ORGANISM(S): Mus musculus 
2013-02-14 | E-GEOD-35833 | biostudies-arrayexpress
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