PREDICTION OF SPLICE SITES IN PLANT PRE-MESSENGER-RNA FROM SEQUENCE PROPERTIES

Heterologous introns are often inaccurately or inefficiently processed in higher plants. The precise features that distinguish the process o f pre-mRNA splicing in plants from splicing in yeast and mammals are u nclear. One contributing factor is the prominent base compositional co ntrast between U-rich plant introns and flanking G + C-rich exons. Inc lusion of this contrast factor in recently developed statistical metho ds for splice site prediction from sequence inspection significantly i mproved prediction accuracy. We applied the prediction tools to re-ana lyze experimental data on splice site selection and splicing efficienc y for native and more than 170 mutated plant introns. In almost all ca ses, the experimentally determined preferred sites correspond to the h ighest scoring sites predicted by the model. In native genes, about 90 % of splice sites are the locally highest scoring sites within the bou nds of the flanking exon and intron. We propose that, in most cases, l ocal context (about 50 bases upstream and downstream from a potential intron end) is sufficient to account for intrinsic splice site strengt h, and that competition for transacting factors determines splice site selection in vivo. We suggest that computer-aided splice site predict ion can be a powerful tool for experimental design and interpretation. (C) 1998 Academic Press Limited.