Evolutionary Fates and Origins of U12-Type Introns

Abstract

U2-type and U12-type introns are spliced by distinct spliceosomes in eukaryotic nuclei. A classification method was devised to distinguish these two types of introns based on splice site sequence properties and was used to identify 56 different genes containing U12-type introns in available genomic sequences. U12-type introns occur with consistently low frequency in diverse eukaryotic taxa but have almost certainly been lost from C. elegans. Comparisons with available homologous sequences demonstrate subtype switching of U12 introns between termini of AT-AC and GT-AG as well as conversion of introns from U12-type to U2-type and provide evidence for a fission/fusion model in which the two splicing systems evolved in separate lineages that were fused in a eukaryotic progenitor.

Determinants of Plant U12-Dependent Intron Splicing Efficiency

“…Introns belonging to these two distinct classes are spliced by two different spliceosomes: the major U2-type spliceosome and the less abundant U12-type spliceosome (Hall and Padgett, 1996;Tarn and Steitz 1996a. Although the first U12 introns to be described had AT-AC-terminal dinucleotides, the majority of U12-type introns contain GT-AG, and a small number contain other noncanonical terminal dinucleotides, such as AT-AA, AT-AG, AT-AT, GT-AT, or GT-GG (Jackson, 1991;Hall and Padgett, 1994;Dietrich et al, 1997Dietrich et al, , 2001aSharp and Burge, 1997;Burge et al, 1998;Wu and Krainer, 1999;Levine and Durbin, 2001;Zhu and Brendel, 2003). Moreover, functional analyses have shown that AT-AC-terminal dinucleotides are not a defining feature of U12 introns (Dietrich et al, 1997(Dietrich et al, , 2001a.…”

“…The most abundant class consists of U2-dependent introns (U2 introns), whereas the second rarer class (<0.4% of introns) consists of U12-dependent introns (U12 introns). U12 introns have been found in the nuclear genomes of vertebrates, plants, and insects (Hall and Padgett, 1994;Sharp and Burge, 1997;Tarn and Steitz, 1997;Krainer, 1998, 1999;Burge et al, 1998;Levine and Durbin, 2001;Patel and Steitz, 2003). Introns belonging to these two distinct classes are spliced by two different spliceosomes: the major U2-type spliceosome and the less abundant U12-type spliceosome (Hall and Padgett, 1996;Tarn and Steitz 1996a.…”

“…Moreover, functional analyses have shown that AT-AC-terminal dinucleotides are not a defining feature of U12 introns (Dietrich et al, 1997(Dietrich et al, , 2001a. Instead, U12 introns contain highly conserved sequences in the 59 splice site (exon:G/ATATCCTY) and branchpoint region (TCCTTRAY) (Hall and Padgett, 1994;Sharp and Burge, 1997;Burge et al, 1998), which are both required for prespliceosome complex formation (Frilander and Steitz, 1999). The 39 splice site consensus sequence of U12 introns (YAC/G:exon) is less informative than their 59 splice site and branchpoint sequences.…”

“…The 39 splice site consensus sequence of U12 introns (YAC/G:exon) is less informative than their 59 splice site and branchpoint sequences. U12 introns also lack a polypyrimidine tract and have a short distance between the branchpoint and 39 splice site (between 10 and 20 nucleotides) (Hall and Padgett, 1994;Burge et al, 1998;Dietrich et al, 2001a;Tarn and Steitz, 1997). In Arabidopsis thaliana, a recent computational search for U12…”

Normal and abnormal mechanisms of gene splicing and relevance to inherited skin diseases

“…Moreover, the natural splice site can also be very different from the consensus sequence, such as U12 introns that start and end with AT-AC [9]. Thus, other information and interactions are often necessary to activate splice site selection.…”