Specialized RNA decay fine-tunes monogenic antigen expression in Trypanosoma brucei

Antigenic variation is an immune evasion strategy used by pathogens, including Trypanosoma brucei. This parasite expresses a single variant surface glycoprotein (VSG) from a large genetic repertoire, which it periodically switches throughout an infection. VSGs are co-transcribed with expression-site-associated genes (ESAGs) within a specialized nuclear body, but there is substantial differential expression and the regulatory mechanisms remain unclear. Here we applied TurboID-mediated proximity labelling mass spectrometry to map the subnuclear expression-site body (ESB) post-transcriptional network. We identify and characterize three previously undescribed components: ESB-associated protein 1 (ESAP1) and ESB-specific proteins 2 and 3 (ESB2 and 3). These proteins form discreet subnuclear condensates that are developmentally regulated. ESB2 is an active RNA endonuclease that negatively regulates ESAG transcripts. Its recruitment depends on a hierarchy involving VEX2, ESAP1 and ESB3, a constant flux of active transcription and RNA processing, and its own nuclease activity. Overall, we uncover a molecular mechanism that fine-tunes expression of virulence genes through specialized RNA decay in T. brucei.