Abstract
During nuclear maturation of most eukaryotic pre-messenger RNAs and long non-coding RNAs, introns are removed through the process of RNA splicing. Different classes of introns are excised by the U2-type or the U12-type spliceosomes, large complexes of small nuclear ribonucleoprotein particles and associated proteins. We created intronIC, a program for assigning intron class to all introns in a given genome, and used it on 24 eukaryotic genomes to create the Intron Annotation and Orthology Database (IAOD). We then used the data in the IAOD to revisit several hypotheses concerning the evolution of the two classes of spliceosomal introns, finding support for the class conversion model explaining the low abundance of U12-type introns in modern genomes.
Highlights
IntroductionIntrons can be excised through two distinct pathways: by the major (greater than 99% of introns in most organisms) or minor (less than 1% in most organisms, with some organisms lacking minor class introns altogether) spliceosome
The process of RNA splicing is a necessary step in the maturation of most eukaryotic pre-messenger RNAs and many long non-coding RNAs
High-confidence U2- and U12-type introns in human were curated from multiple sources and used to generate type-specific position-weight matrices (PWMs) for the 5’ splice site and branch point sequences
Summary
Introns can be excised through two distinct pathways: by the major (greater than 99% of introns in most organisms) or minor (less than 1% in most organisms, with some organisms lacking minor class introns altogether) spliceosome. It was originally thought that the two classes of introns were distinguished by their terminal dinucleotides, with introns recognized by the major spliceosome beginning with GT and ending with AG, and introns recognized by the minor spliceosome beginning with AT and ending with AC. It was later shown that introns in both classes can have either sets of terminal dinucleotides and that longer sequence motifs recognized by the snRNA components unique to each spliceosome distinguish the two classes of introns, the designations of “U2-type” for the major and “U12-type” for the minor spliceosomes [7]
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