ArticleNucleic acids research2015
Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 49 citations in OpenAlex.
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- Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.RNA (New York, N.Y.) · 2025Article
- The plant siRNA landscape.The Plant cell · 2024Review
- tRNA renovatio: Rebirth through fragmentation.Molecular cell · 2023Review
- Insights into the structure and function of the RNA ligase RtcB.Cellular and molecular life sciences : CMLS · 2023Review
- New insights into RNA processing by the eukaryotic tRNA splicing endonuclease.The Journal of biological chemistry · 2023Review
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- The RNA repair proteins RtcAB regulate transcription activator RtcR via its CRISPR-associated Rossmann fold domain.iScience · 2022Article
- Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex.Wiley interdisciplinary reviews. RNA · 2022Review
- Yeast Dxo1 is required for 25S rRNA maturation and acts as a transcriptome-wide distributive exonuclease.RNA (New York, N.Y.) · 2022Article
- Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations.Biomolecules · 2022Review
- Innate, translation-dependent silencing of an invasive transposon in Arabidopsis.EMBO reports · 2022Article
- Article
- TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization.Nucleic acids research · 2021Article
- cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3'RNA biology · 2021Article
- Use of NAD tagSeq II to identify growth phase-dependent alterations inProceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA cleavage by some endoribonucleases and self-cleaving ribozymes produces RNA fragments with 5'-hydroxyl (5'-OH) and 2',3'-cyclic phosphate termini. To identify 5'-OH RNA fragments produced by these cleavage events, we exploited the unique ligation mechanism of Escherichia coli RtcB RNA ligase to attach an oligonucleotide linker to RNAs with 5'-OH termini, followed by steps for library construction and analysis by massively parallel DNA sequencing. We applied the method to RNA from budding yeast and captured known 5'-OH fragments produced by tRNA Splicing Endonuclease (SEN) during processing of intron-containing pre-tRNAs and by Ire1 cleavage of HAC1 mRNA following induction of the unfolded protein response (UPR). We identified numerous novel 5'-OH fragments derived from mRNAs: some 5'-OH mRNA fragments were derived from single, localized cleavages, while others were likely produced by multiple, distributed cleavages. Many 5'-OH fragments derived from mRNAs were produced upstream of codons for highly electrostatic peptides, suggesting that the fragments may be generated by co-translational mRNA decay. Several 5'-OH RNA fragments accumulated during the induction of the UPR, some of which share a common sequence motif that may direct cleavage of these mRNAs. This method enables specific capture of 5'-OH termini and complements existing methods for identifying RNAs with 2',3'-cyclic phosphate termini.
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Registered trials
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.