Architectural limits on split genes

Abstract

Exon͞intron architecture varies across the eukaryotic kingdom with large introns and small exons the rule in vertebrates and the opposite in lower eukaryotes. To investigate the relationship between exon and intron size in pre-mRNA processing, internally expanded exons were placed in vertebrate genes with small and large introns. Both exon and intron size inf luenced splicing phenotype. Intron size dictated if large exons were efficiently recognized. When introns were large, large exons were skipped; when introns were small, the same large exons were included. Thus, large exons were incompatible for splicing if and only if they were f lanked by large introns. Both intron and exon size became problematic at Ϸ500 nt, although both exon and intron sequence inf luenced the size at which exons and introns failed to be recognized. These results indicate that present-day gene architecture ref lects at least in part limitations on exon recognition. Furthermore, these results strengthen models that invoke pairing of splice sites during recognition of pre-mRNAs, and suggest that vertebrate consensus sequences support pairing across either introns or exons.Vertebrate genes are typically split into numerous small exons (average size, 134 nt) interrupted by much larger introns (1). Large introns present problems for initial splice site recognition via models that postulate interactions between factors that concertedly recognize the 5Ј and 3Ј splice sites located at intron termini. In vitro, interactions between the ends of introns have been observed during early spliceosome assembly both in yeast and in mammalian systems (reviewed in refs. 2-7). Most experiments with the mammalian system have utilized premRNAs with internally deleted introns. Extrapolation of results from experiments with precursor RNAs containing small introns to more natural pre-mRNAs with large introns is difficult. An alternate spliceosome assembly mode for premRNAs with small exons and large introns (reviewed in refs. 5-7), which we have termed exon definition, suggests that the earliest interactions between 3Ј and 5Ј splice sites occurs across exons rather than across introns. In vitro expansion of an internal exon to Ͼ300 nt severely inhibits the ability to detect ATP-dependent spliceosome formation (8), suggesting an experimental limit on exon size during exon definition that agreed well with known vertebrate exon sizes. Few experiments have addressed the ability of the in vivo vertebrate splicing machinery to recognize large exons.Large exons are only a rarity in vertebrates. Lower eukaryotes have an inverted exon͞intron architecture compared with higher eukaryotes such that many genes have small introns and large exons (1). Thus, many Schizosaccharomyces pombe or Caenorhabditis elegans genes have introns smaller than 100 nt, and Ϸ50% of the introns in Drosophila melanogaster are Ͻ100 nt. Expansion of such small introns in both S. pombe and D. melanogaster causes either a loss of splicing or incorrect splicing via utilization of cryptic spli...

A computational analysis of sequence features involved in recognition of short introns

“…This approach has been applied to analyze recognition of short introns in five different eukaryotes: yeast, C. elegans, Drosophila, Arabidopsis, and human. Short introns may represent a distinct class of introns that are spliced by an intron definition mechanism (3,21).…”

Genome-wide survey of Alternative Splicing in Sorghum Bicolor

“…An additional illustration of the effect of exon-intron architecture on AS is revealed when the size of mammalian exons is examined. Usually, enlarged exons lead to exon skipping, but if the flanking introns are short, the enlarged exon is included (Sterner et al 1996). The average intron size in S. bicolor was close to rice and Brachypodium intron size (433 bp) and longer than the average intron size (173 bp) of Arabidopsis (Wang and Brendel 2006).…”

Coevolutionary networks of splicing cis -regulatory elements

“…Two general models have been proposed for early spliceosome assembly (5). In the intron definition model, intron-spanning interactions between factors recognizing the 5Јss and the downstream 3Јss occur initially; this model is supported for transcripts with large exons and small introns (6,7). In the exon definition model, exon-spanning interactions between factors that recognize the 5Јss and factors bound at the upstream 3Јss lead to formation of exon definition complexes before rearrangements that yield intron-spanning spliceosomes.…”