Intronic RNA: Ad'junk' mediator of post-transcriptional gene regulation

Abstract

RNA splicing, the process through which intervening segments of noncoding RNA (introns) are excised from pre-mRNAs to allow for the formation of a mature mRNA product, has long been appreciated for its capacity to add complexity to eukaryotic proteomes. However, evidence suggests that the utility of this process extends beyond protein output and provides cells with a dynamic tool for gene regulation. In this review, we aim to highlight the role that intronic RNA plays in mediating specific splicing outcomes in pre-mRNA processing, as well as explore an emerging class of stable intronic sequences that have been observed to act in gene expression control. Building from underlying flexibility in both sequence and structure, intronic RNA provides mechanisms for post-transcriptional gene regulation that are amenable to the tissue and condition specific needs of eukaryotic cells. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.

Fig. 1.

The role of RNA structure in pre-mRNA splicing. A) Canonical consensus sequences with a pre-mRNA that mediate splicing: The 5ss (purple), Branchpoint sequence (maroon), polypyrimidine tract (blue), and 3ss (orange). Splicing proceeds through a two-step transesterification reaction. In the first step the 2′OH of the branchpoint carries out a nucleophilic attack (represented by red arrow) on the 5ss, while in the second step the 3′OH of the 5′ exon attacks the first nucleotide downstream of the 3ss. B) Diagram of structures with inhibitory effects on splicing. Local stem loops repress the binding of U1 and U2 snRNPs at the 5ss and 3ss respectively, by pairing cis-elements within the double stranded structures. C) Diagram of structures that promote efficient splicing. Local stem loops serve to bring important cis-elements (such as the 5ss and branchpoint, as well as the branchpoint and 3ss) into closer proximity to one another, which promotes the interaction between snRNPs. D) Diagram of long range intra-intronic repeat elements (yellow) which pair flanking ends of intron to promote efficient splicing. Such pairings are suggested to obviate the need for essential splicing elements (such as the U2AF heterodimer). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2.

Schematic of Lariat Processing and sisRNA Accumulation/Function. A) Following splicing both a ligated exon product and intronic lariat are produced. The lariat is typically debranched by the debranching enzyme (DBR1:light purple) and processed for degradation in the nucleus by exonucleases (green). However, some stable lariats persist in both the nuclease and cytoplasm. Export to the cytoplasm proceeds through the NXF1/NXT1 system (dark purple) and leads to the accumulation of both stable lariat RNAs with trimmed tails and linearized intronic segments. B) sisRNAs have been show to work in trans (left hand portion of the panel) to control post-transcriptional processing by acting as molecular sponges, or sinks, for proteins (orange hexagons) including splice and RNA processing factors. Additionally the accumulation of snRNPs on stable lariats is suggested to cause global changes in RNA splicing efficiency. sisRNAs are also known to function in cis (right hand portion of the panel) to both positively and negatively mediate the expression of their host genes through feedback loops. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)