Prediction of splice sites in plant pre-mRNA from sequence properties

Abstract

Heterologous introns are often inaccurately or inef®ciently processed in higher plants. The precise features that distinguish the process of premRNA splicing in plants from splicing in yeast and mammals are unclear. One contributing factor is the prominent base compositional contrast between U-rich plant introns and¯anking G C-rich exons. Inclusion of this contrast factor in recently developed statistical methods for splice site prediction from sequence inspection signi®cantly improved prediction accuracy. We applied the prediction tools to re-analyze experimental data on splice site selection and splicing ef®ciency for native and more than 170 mutated plant introns. In almost all cases, the experimentally determined preferred sites correspond to the highest scoring sites predicted by the model. In native genes, about 90% of splice sites are the locally highest scoring sites within the bounds of the¯anking exon and intron. We propose that, in most cases, local context (about 50 bases upstream and downstream from a potential intron end) is suf®cient to account for intrinsic splice site strength, and that competition for transacting factors determines splice site selection in vivo. We suggest that computer-aided splice site prediction can be a powerful tool for experimental design and interpretation.

Alternative Splicing Studies of the Reactive Oxygen Species Gene Network inPopulusReveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase

“…High degrees of sequence similarity around these sites were found to sequences reported for Arabidopsis and rice (Reddy, 2007). These sites are different in human and mouse genes, suggesting that splice site preferences in plants and animals also differ (Wiebauer et al, 1988;Brendel et al, 1998;Reddy, 2007).…”

Expression of Genomic AtCYCD2;1 in Arabidopsis Induces Cell Division at Smaller Cell Sizes: Implications for the Control of Plant Growth

“…1). In plants, more than other taxa, cDNA transgenes appear to be at risk of incomplete expression from reformed splice boundaries because AGGT motifs can be spliced without requiring flanking sequences that mark introns in other kingdoms (Brendel et al, 1998).…”

Natural rules for Arabidopsis thaliana pre-mRNA splicing site selection

“…Several different computer-aided splicing site selection models that were believed to mimic the in vivo splicing process mathematically have been developed based on several key factors. These factors include: the consensus splicing site sequence, intronic U-rich sequence, and the branch point confirmed through the different species (vertebrate, yeast) [9,10,15,18]. However, the rules and mechanisms for plant pre-mRNA splicing remain unknown.…”