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Ribosome profiling of WT vs Cas9-based DBP1 deletion

ABSTRACT: Ribosome profiling of WT vs Cas9-based DBP1 deletion

PROVIDER: PRJNA1094945 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28516838.fastq.gz	Fastqsanger.gz
	SRR28516839.fastq.gz	Fastqsanger.gz
	SRR28516840.fastq.gz	Fastqsanger.gz
	SRR28516841.fastq.gz	Fastqsanger.gz
	SRR28516842.fastq.gz	Fastqsanger.gz

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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

loss of DBP1 during meiosis in yeast

Project description: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.

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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.

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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

DBP1 in budding yeast

Project description:DBP1 in budding yeast

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

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

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Transcription profiling of Saccharomyces cerevisiae eIF4G isoforms to investigate eIF4G deletion ribosome occupancy

Project description:Effect of eIF4G gene deletion on the ribosome occupancy.

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Xrn1-sensitive lncRNAs are globally insensitive to the cytoplasmic helicases Ecm32, Ski2, Slh1, Dbp1 and Dhh1

Project description:To investigate the role of cytoplasmic helicases in the decay of Xrn1-sensitive lncRNAs, we performed RNA-Seq in WT, ecm32-delta, ski2-delta, slh1-delta, dbp1-delta and dhh1-delta yeast cells.

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loss of DBP1 during meiosis in yeast

Project description:loss of DBP1 during meiosis in yeast

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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.

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