FINDING OF U12-TYPE INTRONS AND OF THEIR PARTNER SNRNAS IN THE Arabidopsis thaliana NUCLEAR GENOME

¹ Laboratory of Plant Physiology & Molecular Biology, UMR-CNRS 5545, University of Perpignan, F-66860 PERPIGNAN cedex, France

² VIB Department of Genetics, University of Ghent, K.L.Ledeganckstraat 35, B-9000 GENT, Belgium

³ INRA-France Associated Laboratory

Rare introns with AT-AC dinucleotide extremities instead of GT-AG, have been reported in animals. Together with their borders, AT-AC introns share unusual consensus at the donor site and around the branch-point. The splicing of these introns follows a spliceosomal mechanism similar to classical U2-type introns, but involving four specific snRNAs: U11, U12, U4atac & U6atac instead of U1, U2, U4 & U6 [1]. Upon sequencing a contig from Arabidopsis we found a gene (SAC1) where one of the 19 introns, intron-7, has AT as donor site and AA as acceptor, a situation never described previously [1]. This AT-AA intron has every features of the animal AT-AC introns. A search in sequence databases revealed other unnoticed cases of AT-AA/C introns in plants, although all with AT-AC borders. Strikingly, intron-7 from the SAC1 gene from rice has GT-AG borders instead of AT-AA, although it keeps the typical U12-type donor and branch-point consensus for splicing. Databases searches performed by us and by others [3] independantly showed other examples of similar U12-type GT-AG introns, both in plants and animals. Mutagenesis experiments of borders of AT-AC introns in animals have indeed demonstrated that these GT-AG introns are spliced using the four specific sn RNAs. Last, a peculiar search for the genes encoding the specific snRNAs required for the splicing of the U12 introns in the Arabidopsis genome sequence allowed us to find likely candidates for them. The existence of these introns is an additional challenge for proper genome annotation. Their finding indicates that the non-canonical introns existed prior to the separation of the animal and plant kingdoms, and must, therefore, be at least 10⁹ years old. That such rare introns have been preserved for so long besides the classical ones suggests that they play an essential role which remains to be discovered. [1] Tarn & Steitz, Trends Biochem. Sci., 1997, 22:132 [2] Wu et al., Nature Genet., 1996, 14:383 [3] Sharpe & Burge, Cell, 1997, 91:875