ArticleRNA (New York, N.Y.)2010
Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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
33 citing papers in PubMed.
- A ribozyme ligase that requires a 3' terminal phosphate on its RNA substrate.Nature communications · 2026Article
- cP-RNA-seq for tRNA half sequencing.Methods in enzymology · 2025Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Middle-out sequence confirmation of CRISPR/Cas9 single guide RNA (sgRNA) using DNA primers and ribonuclease T1 digestion.Analytical and bioanalytical chemistry · 2023Article
- Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations.Biomolecules · 2022Review
- cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3'RNA biology · 2021Article
- Ligation of 2', 3'-cyclic phosphate RNAs for the identification of microRNA binding sites.FEBS letters · 2021Article
- Physiologic RNA targets and refined sequence specificity of coronavirus EndoU.RNA (New York, N.Y.) · 2020Article
- Genome-wide identification of short 2',3'-cyclic phosphate-containing RNAs and their regulation in aging.PLoS genetics · 2019Article
- Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities.Current opinion in biotechnology · 2019Review
- The role of RNA modifications in the regulation of tRNA cleavage.FEBS letters · 2018Review
- Genetic bypass of essential RNA repair enzymes in budding yeast.RNA (New York, N.Y.) · 2018Article
- Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome.Frontiers in genetics · 2018Review
- An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus.Scientific reports · 2017Article
- Cleavage of 3'-terminal adenosine by archaeal ATP-dependent RNA ligase.Scientific reports · 2017Article
- Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors.Genes & development · 2017Review
- Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method.Nature protocols · 2016Article
- Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing.Nucleic acids research · 2015Article
- Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA.Nature methods · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The combination of ligation-based RNA capture methods and high-throughput sequencing has facilitated the characterization of transcriptomes and the identification of novel noncoding RNAs. However, current ligation-based RNA capture methods require RNA substrates with terminal 3'-hydroxyl groups, limiting their utility for identifying RNAs with modified termini like 2',3'-cyclic phosphates. Cyclic phosphate-terminated RNAs are generated by endonucleolytic cleavages and self-cleaving ribozymes and are found as stable modifications on cellular RNAs such as the U6 spliceosomal RNA. We developed a method that uses the Arabidopsis thaliana tRNA ligase to add an adaptor oligonucleotide to RNAs that terminate in 2',3'-cyclic phosphates. The adaptor allows specific priming by reverse transcriptase, which is followed by additional steps for PCR amplification and high-throughput DNA sequencing. Applying the method to total human RNA, we found 2836 sequencing reads corresponding to the 3' terminus of U6 snRNA, validating the method. In addition to a large background of reads that map throughout abundantly transcribed RNAs, we also found 42,324 reads of specific fragments from several tRNA isoacceptor families, suggesting that this method may identify processing events previously undetected by other RNA cloning techniques.
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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.