Comprehensive database and evolutionary dynamics of U12-type introns

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.

Figure 1.

(A) Overview of the major steps of the intronIC algorithm. (B) Scatter plot of all classified introns in the human genome; gray: U2-type introns, red: U12-type introns with probability scores ≤84%; yellow: U12-type introns with probability scores from 84–90%, green: U12-type introns with probability scores >90%, our chosen scoring threshold. (C) Sequence logos of the 5′SS and BPS PWMs for GT-AG/AT-AC U2- and U12-type introns. (D) Balanced accuracy performance of the classifier with different values of hyperparameter C on test sets during the first round of the cross-validation process. (E) Histogram (with logarithmic scale y-axis) of probability scores for the human data shown in part B.

Figure 2.

Phylogenetic distribution of U12-type introns in all species annotated by the Intron Annotation and Orthology Database (IAOD), U12DB (18), SpliceRack (35) and ERISdb (24). Blank entries in the table represent organisms not represented in the respective database. Counts of U12-type introns in the IAOD only represent introns flanked by coding exons. The NCBI Taxonomy Browser (70) and Integrative Tree of Life (71) were used to create the phylogenetic tree.

Figure 3.

Phase distribution of introns within each class in all genomes annotated in the IAOD. Organisms are grouped by phylogeny. The bias against phase 0 U12-type introns is statistically significant in all organisms but G. max, O. sativa, X. tropicalis and Z. mays (chi-squared; P < 0.10). The bias toward phase 0 U2-type introns is statistically significant in all organisms but A. mellifera, D. melanogaster, S. cerevisiae and S. pombe (chi-squared; P < 0.10).

Figure 4.

Percentages of introns with the specified nucleotide immediately upstream of the 5′ splice site in each phase of both classes of introns. Organisms are grouped by phylogeny.

Figure 5.

Nucleotide biases at the -1 position relative to the 5′ splice site for all organisms (excluding those lacking U12-type introns) annotated in the IAOD, grouped by terminal dinucleotides and intron class.