Characterization of the genes encoding U4 small nuclear RNAs in Arabidopsis thaliana

Three genes encoding U4 small nuclear RNA (U4 snRNA) in the higher plant Arabidopsis thaliana have been isolated and characterized. Two of the genes, AtU4.1 and AtU4.2, contain all the transcriptional signals known to be essential for U-snRNA gene activity in dicot plants: the Upstream Sequence Element (USE), the -30 TATA box and the downstream 3' end formation sequence. The USE and TATA elements are centered approximately four helical DNA turns apart, a feature characteristic of RNA polymerase II-transcribed U-snRNA genes of plants. The genes AtU4.1 and AtU4.2 are actively transcribed in transfected plant protoplasts and in Arabidopsis plants. Expression of the third gene, AtU4.3, could not be demonstrated. Since this gene is missing the downstream signal important for RNA 3' end formation, it probably represents a pseudogene. The genes AtU4.1 and AtU4.2 encode 152-153 nt long RNAs which show 85-89% sequence similarity with broad bean and pea U4 RNAs and 60-65% similarity with mammalian U4 RNAs. Arabidopsis U4 and U6 snRNAs can be folded into the base-paired Y-shaped model supporting the importance of the U4/U6 interaction during pre-mRNA splicing in plants as well as animals.