A non-coding role for trypanosome VSG transcripts in allelic exclusion

Bloodstream-form African trypanosomes display antigenic variation. This requires mono-telomeric but switchable expression of a Variant Surface Glycoprotein (VSG) gene in a transcription and splicing compartment that is inter-chromosomally bridged by VSG exclusion factors 1 and 2 (VEX1-2). The dominant gene produces 10 000 times more transcript than excluded VSGs. Additional chromatin and RNA-associated factors are required to maintain VSG exclusion, but our understanding of the mechanisms involved remains incomplete. Here, we show that the VSG transcript impacts allelic competition. We induced either specific translation blockade by recruiting MS2 coat protein to the active VSG 5'-untranslated region, or VSG transcript depletion using RNA interference. Neither perturbation substantially compromised exclusion of native VSGs. In contrast, a VSG transgene escaped exclusion specifically when the native transcript was transiently depleted. While both perturbations blocked cytokinesis, DNA replication and mitosis continued when the transcript, which is stabilized by a cyclin-like F-box protein, was translationally blocked. The proportion of nuclei with a second VEX2 focus was significantly increased in cells with a second active VSG. We conclude that the VSG transcript is a bifunctional coding and non-coding RNA that participates in allelic competition to establish exclusion, a form of RNA-mediated symmetry breaking that also remodels nuclear architecture.