ArticleNature protocols2016
Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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Who cites it
32 citing papers in PubMed, 62 citations in OpenAlex.
- A streamlined, nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing.Cell reports methods · 2026Article
- Regulation of co-translational mRNA decay by PAP and DXO1 in Arabidopsis.BMC plant biology · 2025Article
- Proper 5'-3' cotranslational mRNA decay in yeast requires import of Xrn1 to the nucleus.PloS one · 2025Article
- The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.Nucleic acids research · 2024Article
- The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAbioRxiv : the preprint server for biology · 2024Article
- Cellular energy regulates mRNA degradation in a codon-specific manner.Molecular systems biology · 2024Article
- Roles of the CCR4-Not complex in translation and dynamics of co-translation events.Wiley interdisciplinary reviews. RNA · 2023Review
- DNA-directed termination of RNA polymerase II transcription.Molecular cell · 2023Article
- Atlas of mRNA translation and decay for bacteria.Nature microbiology · 2023Article
- Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.Molecular cell · 2023Article
- Genome-Wide Mapping of 5' Isoforms with 5'-Seq.Current protocols · 2023Article
- Translating across kingdoms: target of rapamycin promotes protein synthesis through conserved and divergent pathways in plants.Journal of experimental botany · 2022Review
- Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential.Molecular cell · 2022Article
- Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells.Cell reports · 2021Article
- High-throughput 5'P sequencing enables the study of degradation-associated ribosome stalls.Cell reports methods · 2021Article
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae.Nucleic acids research · 2021Article
- Improved computational analysis of ribosome dynamics from 5'P degradome data using fivepseq.NAR genomics and bioinformatics · 2020Article
- Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo.Nucleic acids research · 2020Article
- Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.Nature communications · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Co-translational mRNA degradation is a widespread process in which 5'-3' exonucleolytic degradation follows the last translating ribosome, thus producing an in vivo ribosomal footprint that delimits the 5' position of the mRNA molecule within the ribosome. To study this degradation process and ribosome dynamics, we developed 5PSeq, which is a method that profiles the genome-wide abundance of mRNA degradation intermediates by virtue of their 5'-phosphorylated (5'P) ends. The approach involves targeted ligation of an oligonucleotide to the 5'P end of mRNA degradation intermediates, followed by depletion of rRNA molecules, reverse transcription of 5'P mRNAs and Illumina high-throughput sequencing. 5PSeq can identify translational pauses at rare codons that are often masked when using alternative methods. This approach can be applied to previously extracted RNA samples, and it is straightforward and does not require polyribosome purification or in vitro RNA footprinting. The protocol we describe here can be applied to Saccharomyces cerevisiae and potentially to other eukaryotic organisms. Three days are required to generate 5PSeq libraries.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.