RiBi project
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Patrick Kemmeren
PROVIDER: E-MTAB-3189 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The RiBi project investigated the role of chromatin factor Spt6 in ribosome biogenesis. In this experiment we performed transcription profiling of Saccharomyces cerevisiae single and double deletion mutants involved in ribosome assembly. The single mutants examined in this experiment were: arx1-deletion, dbp7-deletion, mrt4-deletion, zuo1-deletion and spt6 -140 mutant. The double mutants were spt6-140 mutant plus arx1-deletion; spt6-140 mutant plus dbp7-deletion; spt6-140 mutant plus mrt4-deletion; spt6-140 mutant plus rsa1-deletion; and spt6- 140 mutant plus zuo1-deletion. The experiment was performed using a dye-swap design where a single wildtype culture was used as a common reference pool.
2017-07-06 | E-MTAB-4574 | biostudies-arrayexpress
Project description:Transcription of eukaryotic genes involves dynamic interactions between RNA polymerases and chromatin that are facilitated by auxiliary factors. One of these chromatin factors is Spt6, encoded by an essential gene that plays regulatory functions throughout all eukaryotes, from yeast to human. We have performed a genetic analysis of Spt6 function by isolating yeast mutations that confer synthetic-lethality to a conditional spt6 allele under permissive conditions. In addition to genes encoding other general transcription factors, such mutations also include genes involved in pre-rRNA processing and ribosomal subunit assembly, among them DBP6 and ARB1. Using an in vivo depletion system for Arb1, the transcriptional response upon the impairment of ribosome assembly, and the potential involvement of Spt6 as a regulator was investigated. Subsequent analyses included the transcriptomic profiles of a set of viable null mutants, lacking genes functionally involved in different steps of ribosome biogenesis. We found that the genes encoding factors directly involved in ribosome assembly change their expression level in response to the impairment of the ribosome biogenesis pathway, and Spt6 plays a role in this regulation by tuning RNA polymerase II transcription during the elongation phase. This regulation does not uniformly affect all ribosome-related genes, since different subsets of genes were induced or repressed in response to different specific malfunctions in ribosome biogenesis. Together, these data extend our understanding of the regulation of ribosome related genes and provide insight into the mechanisms by which defects in ribosome biogenesis lead to a specific regulation of their expression at the level of transcription elongation.
2017-06-05 | GSE64921 | GEO
Project description:Transcription profiling by array of yeast single and double deletion mutants of gene-specific transcription factors
| PRJNA182291 | ENA
Project description:S. pombe nucleophosmin proteins have other functions in addition to the established role in ribosome biogenesis. Indeed, Fkbp39 contributes to silencing of centromeric and subtelomeric heterochromatic transcripts and displays a negative genetic interaction with the RNAi pathway. While the mechanisms of Fkbp39 action on heterochromatin and the negative genetic interaction with RNAi require further investigation, in this study we show that argonaute deletion cells have defects in transcription, shedding light on previously uncharacterized roles of RNAi.
2024-06-25 | GSE179514 | GEO
Project description:To investigate the glucose regulatory system in Saccharomyces cerevisiae, we conducted a time-course in which glucose-depleted wildtype (WT) cells were inoculated into fresh media (SC, 2% glucose). Their subsequent transcriptional output was monitored over a period of five hours by DNA microarrays: samples for gene expression profiling were taken immediately after, as well as 3, 7.5, 15, 30, 60, 110, 150, and 300 minutes after inoculation into fresh medium. Transcripts upregulated are involved in translational processes such as the GO biological processes “ribosome biogenesis” and “ribosome localization”. Transcripts downregulated are enriched for the GO biological processes “cellular respiration” and various metabolism related processes. The time-course was used to verify the physiological relevance of gene expression profiles determined for individual deletions of glucose regulatory system components. Importantly, transcripts up- or downregulated in WT cells upon the addition of glucose are similarly up- or downregulated in deletion mutants that each lack a component of the glucose regulatory system.
2012-06-18 | GSE33098 | GEO
Project description:We did transcription profiling on the effect of pmt1 pmt4 deletion, genes involved in the O-glycosylation process. These mutants cells show inhibition of mating, filamentation and induction of cell wall compensatory mechanism.
2010-09-30 | GSE12182 | GEO
Project description:We did transcription profiling on the effect of pmt1 pmt2 deletion. These genes are involved in the O-glycosylation process. These mutants cells show inhibition of mating, filamentation and induction of cell wall compensatory mechanism.
2010-09-30 | GSE12181 | GEO
Project description:To investigate the glucose regulatory system in Saccharomyces cerevisiae, we conducted a time-course in which glucose-depleted wildtype (WT) cells were inoculated into fresh media (SC, 2% glucose). Their subsequent transcriptional output was monitored over a period of five hours by DNA microarrays: samples for gene expression profiling were taken immediately after, as well as 3, 7.5, 15, 30, 60, 110, 150, and 300 minutes after inoculation into fresh medium. Transcripts upregulated are involved in translational processes such as the GO biological processes “ribosome biogenesis” and “ribosome localization”. Transcripts downregulated are enriched for the GO biological processes “cellular respiration” and various metabolism related processes. The time-course was used to verify the physiological relevance of gene expression profiles determined for individual deletions of glucose regulatory system components. Importantly, transcripts up- or downregulated in WT cells upon the addition of glucose are similarly up- or downregulated in deletion mutants that each lack a component of the glucose regulatory system. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used for each separate hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Two overnight WT cultures were used to inoculate 50 ml cultures at an OD600 of 0.15. These were depleted of glucose by growing for 24 hours and were used the next day to inoculate 500 ml cultures in fresh medium to an OD600 of 0.15. Samples for expression profiling were taken immediately after, as well as 3, 7.5, 15, 30, 60, 110, 150, and 300 minutes after inoculation into fresh medium.
2012-06-17 | E-GEOD-33098 | biostudies-arrayexpress
Project description:Phenotypic and genotypic description of AUTS2 deletion patients found by Array analysis in an international cohort of intellectual disability (ID) and multiple congenital malformations (MCA).
2012-07-12 | GSE37141 | GEO
Project description:Phenotypic and genotypic description of AUTS2 deletion patients found by Array analysis in an international cohort of intellectual disability (ID) and multiple congenital malformations (MCA).
2012-07-12 | GSE37142 | GEO