Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events
Figure 1
Basic Steps of Pre-mRNA Splicing and Patterns of Alternative Exons
(A) Five small nuclear ribonucleoproteins (snRNPs U1, U2, U4, U5, and U6), an auxiliary splicing factor (U2AF), and many other factors (not represented) organized in the human spliceosome execute the excision of introns. After the recognition of 5′ss, 3′ss, and branch point, respectively, by U1, U2AF, and U2, the intron is first cleaved at the 5′ss and subsequently at the 3′ss, mediated by U4/U6 and U5 (U1, U2, and U4 are detached later during the cycle). The intron remains in the nucleus and is degraded, while ligated exons are transported outside to the cytoplasm.
(B) AS events can be inferred by spliced alignments of mRNAs to genomic DNA (cf. Figure 3), indicated by dashed lines (AS part of exon colored in black), and commonly distinguished in terms of whether mRNA isoforms differ by skipping of an exon (SE), or whether isoforms differ in the usage of a 5′ss or 3′ss, producing an A5E or A3E, respectively. A fourth type, termed retention-type intron, occurs when two isoforms differ by the presence of an unspliced intron in one transcript that is spliced in the other.
(C) More complex types of AS forms can be constructed from canonical splice variants; different isoforms can also be the result of variations at the 5′- and 3′-terminus of transcripts, which are not necessarily due to AS.