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.

2025-05-14 | GSE230204 | GEO

Analysing environmentally induced genome-wide frameshift in S. cerevisiae using ribosome profiling

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 Ribosome profiling (Ingolia, et.al 2009, PMID: 19213877), in S.cerevisiae in low nutrients condition. Our goal with Ribosome profiling was to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

2025-05-14 | GSE230203 | GEO

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

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.

2025-05-14 | GSE230202 | GEO

programmed ribosomal frameshift

Project description:programmed ribosomal frameshift Raw sequence reads

| PRJNA310019 | ENA

Environmentally-induced epigenetic conversion of a piRNA cluster

Project description:Environmentally-induced epigenetic conversion of a piRNA cluster

| PRJNA477333 | ENA