AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes.

Abstract

Shortly after the discovery of split genes in 1977, a conserved sequence feature at both ends of cellular and viral introns was recognized, i.e., the presence of GT at the 5′ splice site and AG at the 3′ splice site, giving rise to the so-called GT-AG rule (8). This rule holds in most cases, but exceptions have been found. For example, GC is occasionally found at the 5′ end of certain introns (Table ​(Table1)1) (38). GC-AG introns are processed by the same splicing pathway as conventional GT-AG introns (3). It had long been assumed that removal of all introns from eukaryotic pre-mRNAs took place by the same splicing pathway, until recent developments demonstrated the existence of a second pre-mRNA splicing pathway. TABLE 1 Compilation of GC-AG intronsa Intron 6 of the gene encoding human P120, a proliferating cell nucleolar antigen, and intron 7 of the gene encoding human CMP, a cartilage matrix protein (matrilin 1), were the first reported examples of introns with AT and AC at the intron ends, instead of GT and AG (38). Intron 6 of the gene encoding Rep-3, a DNA repair protein, and intron 2 of the gene encoding Prospero, a Drosophila melanogaster homeodomain transcription factor, also have AT-AC ends (28). In addition to their distinctive dinucleotide ends, these and other AT-AC introns have highly conserved 5′-splice-site and presumptive branch site 8-nucleotide sequence elements that are not present in the major class of introns, ATATCCTY and TCCTTRAY, respectively. On the basis of these sequence features, it was proposed that the minor U11 and U12 snRNAs, which have regions of complementarity to these elements, are required for splicing of AT-AC introns (28). Important aspects of this prediction were soon verified experimentally (29, 100), and two additional minor snRNAs involved in the novel pre-mRNA splicing pathway were discovered (101). The AT-AC splicing pathway was originally named after the distinctive sequences of the intron ends (100). It was later found that a few introns with AT-AC ends are processed by the major pathway (120) and, conversely, that some introns with GT-AG ends are spliced by the minor pathway (18). Therefore, the name AT-AC no longer reflects the dinucleotide intron ends per se, but rather it refers to the minor pathway itself. An alternative designation for the two pathways—U2 dependent and U12 dependent—reflects their observed or expected requirements for one of the four snRNAs specific to each pathway (86).