Competition of RNA splicing: line in or circle up.

Abstract

The advent of high throughput technologies has revealed that mammalian genomes are pervasively transcribed, most for long noncoding RNAs (lncRNAs, at least 200 nt long). Thousands of lncRNAs from intergenic regions (large intergenic noncoding RNA, lincRNA) have been uncovered by massive deep sequencing from the repertoire of polyadenylated (poly(A)+) RNAs, together with multiple chromatin landscapes. These lncRNAs are messenger RNA (mRNA)-like, with linear signatures of 5′ mG caps and 3′ poly(A)+ tails. Unexpectedly, mammalian transcriptomes are even more complex with the expression of RNAs without polyadenylated tails (poly(A)– RNAs) [1], leading to the identification of new lncRNA formats, such as circular RNAs. Due to the covalently close structure and without 3′ poly(A) tails, circular RNAs failed to be analyzed in most transcriptome analyses mainly for polyadenylated RNAs. By taking advantage of deep sequencing from nonpolyadenylated RNA population [1], thousands of circular RNAs were identified to be widely expressed in human cell lines. There are at least two different types of circular RNAs processed from pre-RNA splicing: one type is derived from spliced introns (circular intronic RNAs) [2] and the other type is from back-spliced exons (exonic circular RNAs) [3]. Circular intronic RNAs (ciRNAs) are produced from introns that fail to be debranched after splicing, but covalently circularized with 2′,5′-phosphodiester bond between a splice donor site and a branch point site. The formation of ciRNAs can be reconstituted in expression vectors with the requirement of consensus motifs flanking 2′,5′-phosphodiester bonds. Importantly, ciRNAs were shown to play an important cis-regulatory role in local gene expression [2]. Exonic circular RNAs (circRNAs) are produced from back-spliced circularization [3]. Unlike (normal) RNA splicing that joins an upstream splice donor site with a downstream splice acceptor site, leading to a linear RNA transcript (Figure 1A), back splicing joins a downstream splice donor site reversely with an upstream splice acceptor site, yielding a circular RNA transcript with 3′,5′-phosphodiester bond at the joint site (Figure 1B). In last decades, only a handful of circRNAs were identified and indicated as byproducts of splicing errors with no function. Until recently, the genome-wide profiling of