ArticleNucleic acids research2014
Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Integrated Analysis of Cross-Link-Ligation Data for the Detection of RNA 2D/3D Structures and Interactions In Vivo.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Chemical crosslinking and ligation methods for in vivo analysis of RNA structures and interactions.Methods in enzymology · 2023Article
- Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers.Genome research · 2022Article
- Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts.Nature communications · 2021Article
- Fusion Genes and RNAs in Cancer Development.Non-coding RNA · 2021Review
- A Review on Recent Computational Methods for Predicting Noncoding RNAs.BioMed research international · 2017Review
- The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection.PLoS genetics · 2016Article
- High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases.RNA (New York, N.Y.) · 2016Article
- Metazoan tRNA introns generate stable circular RNAs in vivo.RNA (New York, N.Y.) · 2015Article
- Developmental analysis of spliceosomal snRNA isoform expression.G3 (Bethesda, Md.) · 2014Article
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Authors and funding
2 authors.
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Abstract
Non-coding (nc)RNAs are important structural and regulatory molecules. Accurate determination of the primary sequence and secondary structure of ncRNAs is important for understanding their functions. During cDNA synthesis, RNA 3' end stem-loops can self-prime reverse transcription, creating RNA-cDNA chimeras. We found that chimeric RNA-cDNA fragments can also be detected at 5' end stem-loops, although at much lower frequency. Using the Gubler-Hoffman method, both types of chimeric fragments can be converted to cDNA during library construction, and they are readily detectable in high-throughput RNA sequencing (RNA-seq) experiments. Here, we show that these chimeric reads contain valuable information about the boundaries of ncRNAs. We developed a bioinformatic method, called Vicinal, to precisely map the ends of numerous fruitfly, mouse and human ncRNAs. Using this method, we analyzed chimeric reads from over 100 RNA-seq datasets, the results of which we make available for users to find RNAs of interest. In summary, we show that Vicinal is a useful tool for determination of the precise boundaries of uncharacterized ncRNAs, facilitating further structure/function studies.
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