ArticleNature protocols2016
Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method.
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 48 papers.
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Who cites it
48 citing papers in PubMed, 72 citations in OpenAlex.
- hY3 RNA binds and inhibits ribosomes and modulates the starvation-induced integrated stress response.Nucleic acids research · 2026Article
- A ribozyme ligase that requires a 3' terminal phosphate on its RNA substrate.Nature communications · 2026Article
- A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).RNA (New York, N.Y.) · 2026Article
- PARP1 regulates the genomic ribonucleotide processing activity of TOP1 to prevent the formation of toxic TOP1-DNA adducts and the associated mutations.bioRxiv : the preprint server for biology · 2026Article
- Profile of tRNA-derived short non-coding RNAs during monocyte differentiation and their role in macrophage survival.RNA biology · 2025Article
- High-throughput assay confirmation of a T-cell receptor pre-mRNA fragment as a blood-based inflammatory breast cancer biomarker.medRxiv : the preprint server for health sciences · 2025Article
- A hormone-dependent tRNA half promotes cell cycle progression via destabilization of p21 mRNA.PLoS biology · 2025Article
- Angiogenin-catalyzed cleavage within tRNA anticodon-loops identified by cP-RNA-seq.Bioscience, biotechnology, and biochemistry · 2025Article
- Review
- TaqMan RT-qPCR for tRNA half quantification.Methods in enzymology · 2025Article
- cP-RNA-seq for tRNA half sequencing.Methods in enzymology · 2025Article
- The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type.BMC biology · 2024Article
- Role of Poly(A)-Binding Protein Cytoplasmic 1, a tRNA-Derived RNA Fragment-Bound Protein, in Respiratory Syncytial Virus Infection.Pathogens (Basel, Switzerland) · 2024Article
- Immunoactive signatures of circulating tRNA- and rRNA-derived RNAs in chronic obstructive pulmonary disease.Molecular therapy. Nucleic acids · 2024Article
- PBOX-sRNA-seq uncovers novel features of miRNA modification and identifies selected 5'-tRNA fragments bearing 2'-O-modification.Nucleic acids research · 2024Article
- Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2.Nucleic acids research · 2024Article
- Rapid and scalable detection of synthetic mRNA byproducts using polynucleotide phosphorylase and polythymidine oligonucleotides.RNA biology · 2024Article
- tRNA renovatio: Rebirth through fragmentation.Molecular cell · 2023Review
- Discovery of the major 15-30 nt mammalian small RNAs, their biogenesis and function.Nature communications · 2023Article
- Small RNA modifications: regulatory molecules and potential applications.Journal of hematology & oncology · 2023Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA digestions catalyzed by many ribonucleases generate RNA fragments that contain a 2',3'-cyclic phosphate (cP) at their 3' termini. However, standard RNA-seq methods are unable to accurately capture cP-containing RNAs because the cP inhibits the adapter ligation reaction. We recently developed a method named cP-RNA-seq that is able to selectively amplify and sequence cP-containing RNAs. Here we describe the cP-RNA-seq protocol in which the 3' termini of all RNAs, except those containing a cP, are cleaved through a periodate treatment after phosphatase treatment; hence, subsequent adapter ligation and cDNA amplification steps are exclusively applied to cP-containing RNAs. cP-RNA-seq takes ∼6 d, excluding the time required for sequencing and bioinformatics analyses, which are not covered in detail in this protocol. Biochemical validation of the existence of cP in the identified RNAs takes ∼3 d. Even though the cP-RNA-seq method was developed to identify angiogenin-generating 5'-tRNA halves as a proof of principle, the method should be applicable to global identification of cP-containing RNA repertoires in various transcriptomes.
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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.