Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Loss of DBP1 during meiosis in yeast

ABSTRACT: We used CRISPR/Cas9 to delete the DBP1 ORF in SK1 budding yeast cells. We then used ribosome profiling and mRNA-seq to observe gene expression profiles of wild-type and dbp1∆ cells during meiosis.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE207267 | GEO | 2022/11/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DBP1 in budding yeast

Project description:DBP1 in budding yeast

| PRJNA436358 | ENA

loss of DBP1 during meiosis in yeast

Project description:loss of DBP1 during meiosis in yeast

| PRJNA854601 | ENA

DBP1 in budding yeast

Project description:We analyzed the effect of deleting the gene encoding putative RNA helicase DBP1 in budding yeast on translational efficiencies (TEs) genome wide in wild-type or ded1-ts (temperature-sensitive allele of DED1) strains by combining ribosome footprint profiling with RNA-seq analysis of mRNA abundance. This study includes a total of 32 samples comprised of 16 RNA-Seq samples (mRNA) and 16 ribosome footprint profiling samples (ribo). Experiment 1 includes 8 samples, comprised of 4 RNA-Seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of the dbp1Δ and ded1-ts dbp1Δ mutant strains, cultured in synthetic complete (SC) medium, following shifts in growth temperature from 30°C to 37°C for 2h. Experiment 2 examines the effect of overexpression of DBP1 in rescuing genome-wide translational defects of a ded1-cs mutant (cold-sensitive allele of DED1) and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1 (dubbed DED1-CS), ded1-cs and ded1-cs overexpressing DBP1 (ded1-cs_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 15°C for 10 min. Experiment 3 examines rescue of translational defects of ded1-ts by DBP1 overexpression and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1(DED1-TS), ded1-ts and ded1-ts overexpressing DBP1 (ded1-ts_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 37°C for 2h.

2018-03-01 | GSE111255 | GEO

Ribosome profiling of mitotic exponential cells expressing either Dbp1 or Ded1, at 30C or 37C

Project description:We replaced the DED1 ORF with DBP1 and tested vegetative growth at 30C or 37C to determine helicase specificity and temperature-dependent effects. We found that DBP1 expressing cells do not downregulate all of the housekeeping genes that DED1 expressing cells normally down regulate at high temperature

2025-01-29 | GSE262933 | GEO

Ribosome profiling of WT vs Cas9-based DBP1 deletion

Project description:Previous deleitons of the DBP1 locus suffered from an off-target effect due to cassette insertion (Powers et al, eLife, 2022). Here, we made a markerless deletion to assess gene expression in meiosis with and without Dbp1. Although it is normally highly expressed in this context, its deletion does not cause a major defect in meiotic progression or gene expression.

2025-01-29 | GSE262935 | GEO

Yeast (S. cerevisiae SK1) Sporulation/Meiosis

Project description:Transription profile of Saccharomyces cerevisiae SK1 cultures undergoing synchronous sporulation. We have measured mRNA levels in synchronized SK1 cells immediately upon transfer to the sporulation medium and every 30 minutes after that for 6 hours. mRNA extracted from these cultures were converted to cDNA and hybridized to microarrays and log2 ratios of hybridization signal of each time point was compared to that of time zero (immediately prior to transfer to the sporulation medium). Keywords: Time course

2008-01-16 | GSE8506 | GEO

Transcription profiling of budding yeast during meiosis to examine the effects of Cdc7p inactivation

Project description:Global effects of Cdc7p inactivation during early budding yeast meiosis

2008-10-02 | E-MEXP-1765 | biostudies-arrayexpress

Use of a ubiquitous gene-editing tool in budding yeast causes off-target repression of neighboring gene protein synthesis

Project description:Precision genome-editing approaches have long been available in budding yeast, enabling introduction of gene deletions, epitope tag fusions, and promoter swaps through a selection-based strategy. Such approaches allow loci to be modified without disruption of coding or regulatory sequences of neighboring genes. Use of this approach to delete DBP1 however, led to silencing of expression and the resultant loss of function for the neighboring gene MRP51. We found that insertion of a resistance cassette to delete DBP1, drove a 5' extended alternative transcript for MRP51 which dampened Mrp51 protein synthesis. Misregulation of MRP51 occurred through an integrated transcriptional and translational repressive long undecoded transcript isoform (LUTI)-based mechanism that was recently shown to naturally regulate gene expression in yeast and other organisms. Cassette-induced MRP51 repression drove all mutant phenotypes we detected in cells deleted for DBP1. Selection cassette-mediated aberrant transcription events are not specific to this locus or a unique cassette but can be prevented by insertion of transcription insulators flanking the cassette. Our study suggests the existence of confounding off-target mutant phenotypes resulting from misregulated neighboring loci following genome edits in yeast. Furthermore, features of LUTI-based regulation are broadly conserved to eukaryotic organisms which indicates the potential that similar misregulation could be unnoticed in other edited organisms as well.

2022-06-24 | MSV000089724 | MassIVE

Ribosome profiling of mitotic exponential cells expressing either 2XDbp1, 1XDbp1, or Ded1

Project description:We replaced the DED1 ORF with DBP1 and inserted this either twice or four times in a diploid cell. We determined that with twice as much DBP1 expressable, the same amount of protein was made as for DED1, and there were few changes in gene expression. The transcripts that were translated better with DED1 were ones with highly structured 5' leaders, consistent with Dbp1 acting as a less effective initiation helicase than Ded1.

2025-01-29 | GSE262934 | GEO

R-loop landscapes in yeast meiosis

Project description:R-loop landscapes in yeast meiosis

| PRJNA705491 | ENA