Prediction of Splice Sites in Plant Pre-mRNA from Sequence
Properties
Volker Brendel, Jürgen Kleffe, Jose C. Carle-Urioste, Virginia Walbot
Journal of Molecular Biology
276(1): 85-104 (Feb 13, 1998)
Abstract
Heterologous introns are often inaccurately or inefficiently processed in
higher plants. The precise features that distinguish the process of
pre-mRNA 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 flanking G+C-rich exons.
Inclusion of this contrast factor in recently developed statistical methods
for splice site prediction from sequence inspection significantly improved
prediction accuracy. We applied the prediction tools to re-analyze
experimental data on splice site selection and splicing efficiency 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
flanking exon and intron. We propose that, in most cases, local context
(about 50 bases upstream and downstream from a potential intron end) is
sufficient to account for intrinsic splice site strength, and that competition
for trans-acting 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.
