RNA-seq following knockdown of ESB2, ESB3 or ESAP1 and overexpression of ESB2 WT or Mutant
undergoes antigenic variation to evade the host immune response. A single Variant-Surface-Glycoprotein (VSG) is expressed from a large genetic repertoire (>2,600 genes) within a specialised expression-site body (ESB). Co-transcribed with the active-VSG are expression-site-associated-genes (ESAGs), involved in key host-parasite interactions, including protecting the parasite from human serum lytic effects, modulating the host's innate immune response and uptake of essential nutrients. Despite expression within the same polycistron, there is a staggering differential expression between ESAGs and VSGs (>140-fold), reflecting the need for much higher levels of VSG expression. However, the molecular mechanism has remained elusive for decades. Here, we identified three new ESB-specific components, which form discreet protein condensates, are developmentally regulated and recruited in a hierarchical manner, assembling a specialised and spatially regulated RNA decay pathway that negatively regulates ESAG transcripts. Notably, our findings suggest a broader role for transcript-specific nucleases in regulating expression of virulence genes.