The spliceosome as a transposon sensor

Abstract

The ability to distinguish self from non-self nucleic acids enables eukaryotes to suppress mobile elements and maintain genome integrity. In organisms from protist to human, this function is performed by RNA silencing pathways. There have been major advances in our understanding of the RNA silencing machinery, but the mechanisms by which these pathways distinguish self from non-self remain unclear. Recent studies in the yeast C. neoformans indicate that transposon-derived transcripts encode suboptimal introns and tend to stall in spliceosomes, which promotes the biogenesis of siRNA that targets these transcripts. These findings identify gene expression signal strength as a metric by which a foreign element can be distinguished from a host gene, and reveal a new function for introns and the spliceosome in genome defense. Anticipating that these principles may apply to RNA silencing in other systems, we discuss strong hints in the literature suggesting that the spliceosome may guide small RNA biogenesis in the siRNA and piRNA pathways of plants and animals.

Keywords: RNA interference; RNA processing; genome defense; pre-mRNA splicing; small RNA; spliceosome; transposon.

Figure 1. Kinetic competition model for siRNA biogenesis in C. neoformans. A kinetic competition between splicing and dsRNA synthesis contributes to the targeting of inefficiently spliced transcripts by siRNA. In this hypothetical example, splicing of a transcript’s first intron stalls at the lariat intermediate stage. The intermediate is processed by the lariat debranching enzyme (Dbr1) and SCANR in order to generate dsRNA, which is converted to siRNA by Dcr1/2. The tendency of transposon-derived transcripts to encode suboptimal splicing features and accumulate in spliceosomes targets them for RNA silencing.

Figure 2. Speculative model for the utilization of incompletely spliced transcripts in Drosophila piRNA biosynthesis. The stalled splicing of transcripts originating from piRNA cluster loci may target them for piRNA biogenesis. Transgenes inserted into dual-strand piRNA clusters are spliced less efficiently than when expressed from euchromatic loci, and they give rise to piRNAs that correspond to both intronic and exonic regions. We speculate that this effect may be caused by sequence features of piRNA clusters, or by their heterochromatin context, as indicated by the presence of Rhino (Rhi), an HP1 variant. The splicing and nuclear export factor UAP56 is required for piRNA production from dual-strand piRNA clusters. UAP56 binds piRNA precursor transcripts and colocalizes with Rhi foci in the nucleus, suggesting that UAP56 targets piRNA precursors to Vasa (Vas), a protein that coordinates piRNA processing in the perinuclear nuage. There are several potential mechanisms by which UAP56, a DEAD box protein, might act in the context of this model. First, it could promote heterochromatinization of piRNA cluster loci by Rhi, as suggested by the fact that nuclear Rhi foci require UAP56. Second, UAP56 could bind to piRNA precursor transcripts in order to cause stalled splicing or to disassemble stalled spliceosomes for downstream processing of the precursors. Finally, UAP56 could mediate the nuclear export of precursor transcripts to Vas. Vas subsequently promotes primary piRNA processing as well as the ping pong amplification cycle, in which primary piRNA acts with the PIWI protein Aub to cleave complementary transcripts (indicated in red) that originate either from the dual-strand piRNA cluster itself or from transposons located elsewhere in the genome. Cleavage defines the 5′ end of a secondary piRNA, whose 3′ end is subsequently trimmed to proper length. Secondary piRNA acts with the distinct PIWI protein Ago3 to cleave piRNA cluster-derived precursor transcripts, thereby amplifying their conversion to mature piRNA.