Fig. 1

Splicing reaction and its regulation. a) Splicing, which occurs in the nucleus of eukaryotic cells, required cis-acting sequences located in the pre-mRNA at the exon/intron and intron/exon junctions: the 5' splice site, the branch point or BP, the polypyrimidine Y tract and 3' splice site. R=purine; N=any nucleotide; Y=pyrimidine. b) Splicing involved two consecutive transesterification reactions carried out by the spliceosomal machinery, which is composed by five small nuclear ribonucleoproteins (U1, U2, U4, U6, and U5 snRNPs). The different complexes formed by snRNPs, pre-mRNA and a large number of proteins (not indicated) are depicted. The final product of the splicing reaction is the mature mRNA in which exons are ligated together, whereas intron is released in the form of a looped structure (the lariat). Thin black lines=introns; blue cylinders=exons. c) Different types of AS reaction: (i) exon skipping; (ii) intron retention; (iii) alternative 3' splice sites (ss); (iv) alternative 5' splice sites (ss); (v) mutually exclusive exons. d) AS regulation requires the combined action of trans- and cis-acting elements. (i) Generally, hnRNPs by binding intronic or exonic splicing silencers (ISS or ESS) directly prevent the recognition of the regulated exon by the spliceosomal machinery (red dashed lines). (ii) On the contrary, exonic or intronic splicing enhancers (ESE or ISE) are bound by SR factors able to stimulate spliceosome assembly on 5' and 3' splice sites (blue dashed lines). (iii) hnRNPs can also polymerize along the exon and displace ESE-bound SR factors, thus preventing exon recognition. (iv) Differently, other SRFs (like NOVA2) are able to promote or repress exon recognition depending on the location of their binding sites on the pre-mRNA. For example, NOVA2 stimulates exon skipping (red dashed lines) when bound to exonic or upstream intronic YCAY (Y=pyrimidine) clusters, while it promotes exon inclusion (green dashed lines) when associated to downstream intronic motifs