Regulation of alternative splicing by short non-coding nuclear RNAs

Abstract

Recent results from deep-sequencing and tiling array studies indicated the existence of a large number of short, metabolically stable, non-coding RNAs. Some of these short RNAs derive from known RNA classes like snoRNA or tRNAs. There are intriguing similarities between short non-coding nuclear RNAs and oligonucleotides used to change alternative splicing events, which usually target a disease-relevant RNA. We review the current knowledge of this emerging class of RNAs and discuss evidence that some of these short RNAs could function in alternative splice site selection.

Figure 1

Examples of regulation by short RNAs. Exons are shown as boxes, introns as lines. The branchpoint is shown as a diamond. Events that generally promote exon inclusion are indicated by black exons, events that lead to exon skipping are indicated by white exons. However, there are numerous exceptions to these rules. (A and B) U1 and U2 snRNP binding promotes exon inclusion. (C and D) Oligonucleotides that block 3′ or 5′ splice sites generally promote exon skipping. (E) Oligonucleotides that target exonic (shown) or intronic enhancers promote exon skipping. (F) Oligonucleotides that target exonic or intronic (shown) silencers promote exon skipping. (G) Bifunctional oligonucleotides can be used to target splicing enhancing proteins to exons, which generally promotes their inclusion. They bind both to RNA and to regulatory proteins (hexagon). (H) Modified U7 constructs can be used to target the 5′ splice site (shown) or splicing enhancers, which typically blocks exon usage. (I) Chimeric U7 constructs that bind both the RNA and to splicing regulators can target splicing enhancing proteins to exons, which generally promotes their inclusion. (K) C/D box snoRNAs and their associated RNPs (circle) can be modified to target the branchpoint where they cause 2′-O-methylation, which results in exon skipping. (L) Riboswitches change conformation upon ligand binding (indicated by the dotted structure and the small circle), which causes release of a previously blocked splice site and subsequent exon inclusion. (M) RNA can form secondary structures in cis, which can promote exon inclusion by removing repressing proteins (small hexagon).

Figure 2

Regulation of serotonin receptor 5-HT2C by HBII -52 derived psnoRNAs. (A) The genomic structure of the 5-HT2C receptor. The arrow in exon III indicated the translational start point. HBII -52 derived psnoRNAs interact with an 18 nucleotide complementarity region in exon Vb. (B) Protein coding parts of the mRNAs derived from different pre-mRNA processing events. Exon Vb skipping results in a shortened mRNA that endodes a truncated protein but is most likely subject to nonsense-mediated mRNA decay. Exon Vb can be edited at five positions (indicated as arrows). The editing event promotes inclusion of the exon, but changes the amino acid sequence at three points. The psnoRNAs cause inclusion of exon Vb without editing, which generates a receptor with the highest agonist efficacy. (C) Structure of the encoded proteins. Editing of exon Vb leads to a change a potentially three amino acids, which are located in the second intracellular loop that couples to the effector G protein. The editing events weaken the receptor-G protein interaction and lead to a weak serotonin response. The non-edited receptor features the amino acids I, N and I at the positions that could be edited and shows the strongest coupling to the G protein and response to serotonin.