VSG Exclusion Protein 2 (VEX2) ChIP-Seq and scRNA-Seq following its depletion in Trypanosoma brucei

UPF1-like helicases play roles in telomeric heterochromatin formation and X-chromosome inactivation and we focus here on variant surface glycoprotein (VSG) exclusion-factor-2 (VEX2), a UPF1-related protein in the African trypanosome. This bloodstream parasite evades host immunity by employing monogenic and switchable VSG expression, a form of antigenic variation which involves transcription of one telomeric VSG gene at a time. A trans-splicing compartment and the single VSG transcription factory are juxtaposed and enriched for VEX1 and VEX2, respectively, but our understanding of the VSG exclusion mechanism remains otherwise incomplete. Here, using ChIP-Seq, we show that VEX2 associates with chromatin specifically at the single active VSG expression site on chromosome 6, forming an allele-selective connection, via VEX1, to the splicing locus on chromosome 9, bridging two chromosomes and the VSG transcription and splicing compartments. Moreover, using single cell transcriptomics (10x Genomics) following VEX2-depletion, we observed simultaneous derepression of >10 distinct telomeric VSGs, revealing the capacity, in the absence of VEX2, for multi-allelic VSG expression in individual cells.