Circular RNA Detection from High-throughput Sequencing

Alternative splicing refers to the production of multiple mRNA isoforms from a single gene due to alternative selection of exons or splice sites during pre-mRNA splicing. While canonical alternative splicing produces a linear form of RNA by joining an upstream donor site (5' splice site) with a downstream acceptor site (3' splice site), a special form of alternative splicing produces a non-coding circular form of RNA (circular RNA) by ligating a downstream donor site (5' splice site) with an upstream acceptor site (3' splice site); i.e., back-splicing. Over the past two decades, many studies have discovered this special form of alternative splicing that produces a circular form of RNA. Although these circular RNAs have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of these studies has been on exonic circular RNAs (circRNAs: donor site and acceptor site are from exon boundaries) and circular intronic RNAs (ciRNAs: donor and acceptor are from a single intron). This type of approach was conducted in the relative absence of methods for searching another group of circular RNAs, or circular complex RNAs (ccRNAs: either the donor site or acceptor site is not from exon boundaries), that contains at least one exon and one or more flanking introns. Studies of ccRNAs would serve as a significant first step in filling this void. In this paper, we developed a new computational algorithm that can detect all three types of circular RNAs. We applied our algorithm on a set of RNA-seq data to examine the composition of circular RNAs in the given dataset. Surprisingly, our results showed that the new type of circular RNA (ccRNA) was the second most common type of circular RNA while circRNA was the most common type as expected.