An excised SV40 intron accumulates and is stable in Xenopus laevis oocytes

Xenopus laevis oocytes injected with simian virus 40 (SV40) DNA synthesize abundant quantities of viral late region RNA. In a previous analysis of the 5' ends of oocyte SV40 late RNAs, it was observed that, in contrast to the majority of the late RNA species, an abundant class of viral late RNAs, whose 5' ends mapped at or near nucleotide 294, was not polyadenylated. The structure of this RNA class has now been characterized further. We have shown that this species consists of a class of small uncapped RNA molecules with heterogeneous 3' ends mapping between nucleotides 417 and 433. This corresponds well with the position of a 139-nucleotide intron within the leader region of late 16S RNA (nucleotides 294-433). The identification of this RNA class as an excised intron was strongly supported by the fact that it displayed anomalous mobilities on different percentage polyacrylamide gels, a property of lariat introns. Furthermore, incubation of oocyte RNA with a HeLa cell extract with lariat debranching activity converted the small RNA to a class that now migrated as less than or equal to 140 nucleotides in length in 8% gels, consistent with the size of the linear intraleader intron. Additional analysis of this RNA showed that it is primarily nuclear in localization and is probably the most stable viral RNA species in the oocyte. These data suggest that oocytes accumulate large quantities of the 16S intraleader intron because of their failure to debranch this RNA efficiently.