Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments

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.

Researchers at the University of North Carolina, Chapel Hill 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, the researchers show that these chimeric reads contain valuable information about the boundaries of ncRNAs. They have developed a bioinformatic method, called Vicinal, to precisely map the ends of numerous fruitfly, mouse and human ncRNAs. Using this method, they analyzed chimeric reads from over 100 RNA-seq datasets, the results of which they make available for users to find RNAs of interest.

Availability – The scripts and instructions are available for download from the following website: https://sites.google.com/site/zhipeng0426/programming.