Where the Minor Things Are: A Survey of Minor Spliceosomal Introns in Thousands of Eukaryotic Genomes

Abstract

Spliceosomal introns are segments of eukaryotic pre-mRNA that are removed (“spliced”) during creation of mature mRNA, and are one of the defining and domain-specific features of gene structure in eukaryotes. Introns are spliced by a large, multisubunit ribonucleoprotein machinery called the spliceosome, and most eukaryotic genomes contain two distinct sets of this machinery—the major (or U2-type) spliceosome is responsible for removal of the vast majority (usually > 99%) of introns in a given genome, with the minor (or U12-type) spliceosome processing the remaining minuscule fraction. Despite in some cases only being responsible for the removal of single-digit numbers of introns in entire genomes, the minor splicing system has been maintained over the roughly 1.5 billion years of eukaryotic evolution since the last eukaryotic common ancestor, and a number of recent studies have suggested that minor introns may be involved in certain aspects of cell cycle regulation and cancer development. It is in this context that we present a broad bioinformatic survey of minor introns across more than 3000 eukaryotic genomes, providing a dramatic increase in information about their distribution in extant species, descriptions of their evolutionary dynamics and features across the eukaryotic tree, and estimates of the minor intron complements of various ancestral nodes.