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

Abstract

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 168 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 :S140 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 168 intraleader intron because of their failure to debranch this RNA efficiently.

Herpes simplex virus latency-associated transcript is a stable intron.

“…An exception is an intron in the late region of SV40, which has been shown (34) to be stable. However, the stability of this intron is seen only in injected Xenopus oocytes, where it may be inefficiently debranched, and not in SV40-infected cells (34). LAT accumulates in infected neurons, in infected tissue culture cells, and in monkey kidney cells transfected with a LAT expression plasmid.…”

Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis

“…We refer to these as ''intronic sequences'' rather than introns because the stored sequences can be considerably shorter than the entire intron from which they are derived. A few specific examples of stable intronic sequences have been described before (Michaeli et al 1988;Kopczynski and Muskavitch 1992;Qian et al 1992;Yang et al 2011), but these have been considered exceptional. To our knowledge, stable intronic sequences derived from a majority of the transcribed genes in the genome have not been previously described.…”

“…Much less is known about the lifetime of introns in tissues. A few cases of stable introns have been described (Michaeli et al 1988;Kopczynski and Muskavitch 1992;Qian et al 1992;Yang et al 2011), although it is generally believed that most introns or intron fragments are unstable. There are some exceptions; notably, the small nucleolar RNAs (snoRNAs), which are derived by debranching of spliced lariats followed by trimming to produce the mature molecule (Ooi et al 1998;Petfalski et al 1998).…”

EBV Noncoding RNAs

“…Studies on cellular sisRNAs in Xenopus oocytes have revealed that many sisRNAs are stable for at least 48 h post-transcription (Gardner et al 2012; Talhouarne and Gall 2014). Interestingly, injection of Xenopus oocytes with SV40 polyomavirus DNA yields a similar, unusually stable nuclear, non-capped, non-polyadenylated, and intronic viral RNA (Michaeli et al 1988), raising the possibility that other DNA tumor viruses might encode sisRNAs. In fact, lariat-derived, stable intronic RNAs have been described for other herpesviruses, such as the ~2-kb latency-associated transcript (LAT) expressed by herpes simplex virus (Bloom 2004), a conserved ~5-kb intron expressed by human cytomegalovirus (hCMV) (Kulesza and Shenk 2004), and a 7.2-kb ortholog, RNA7.2, expressed by mouse CMV, which facilitates persistent viral replication in vivo (Kulesza and Shenk 2006).…”