The establishment of variant surface glycoprotein monoallelic expression revealed by single-cell RNA-seq ofTrypanosoma bruceiin the tsetse fly salivary glands

The long and complexTrypanosoma bruceidevelopment in the tsetse fly vector culminates when parasites gain mammalian infectivity in the salivary glands. A key step in this process is the establishment of monoallelic variant surface glycoprotein (VSG) expression and the formation of the VSG coat. The establishment of VSG monoallelic expression is complex and poorly understood, due to the multiple parasite stages present in the salivary glands. Therefore, we sought to further our understanding of this phenomenon by performing single-cell RNA-sequencing (scRNA-seq) on these trypanosome populations. We were able to capture the developmental program of trypanosomes in the salivary glands, identifying populations of epimastigote, gamete, pre-metacyclic and metacyclic cells. Our results show that parasite metabolism is dramatically remodeled during development in the salivary glands, with a shift in transcript abundance from tricarboxylic acid metabolism to glycolytic metabolism. Analysis ofVSGgene expression in pre-metacyclic and metacyclic cells revealed a dynamicVSGgene activation program. Strikingly, we found that pre-metacyclic cells contain transcripts from multipleVSGgenes, which resolves to singularVSGgene expression in mature metacyclic cells. Single molecule RNA fluorescencein situhybridisation (smRNA-FISH) ofVSGgene expression followingin vitrometacyclogenesis confirmed this finding. Our data demonstrate that multipleVSGgenes are transcribed before a single gene is chosen. We propose a transcriptional race model governs the initiation of monoallelic expression.