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Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria using 5PSeq

ABSTRACT: Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria using 5PSeq

PROVIDER: PRJNA957826 | ENA |

REPOSITORIES: ENA

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Analysing environmentally induced genome-wide frameshift

Project description:Analysing environmentally induced genome-wide frameshift

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Project description:In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To measure the RNA degradation, we utilized SLAM-seq (Herzog, et.al, 2017, PMID: 28945705) in S.cerevisiae in wildtype and NMD mutant (upf1Δ). Our goal with SLAM-seq is to quantify the fraction of the transcriptome that is directly degraded as a result of environmentally induced ribosome frameshifts through an NMD-dependent mechanism.

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Project description:In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation.To explore this process, we utilized HT-5PSeq (Zhang & Pelechano, 2021, PMID:35474692) to measure the ribosome footprint of co-translationally degraded mRNAs in S.cerevisiae under different stresses in YPD and CSM (poor nutrients). To show the mechanism is conserved in bacteria, we performed HT-5PSeq in B.subtilis upon starvation .Our goal with HT-5PSeq is to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

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Analysing environmentally induced genome-wide frameshift

Project description:This SuperSeries is composed of the SubSeries listed below.

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