This repository contains the data for the manuscript https://doi.org/10.1038/s41564-020-00833-4. The HiC analysis pipeline can be found at https://github.com/bgbrink/PRJEB35632. Abstract Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance of persistent infections. African trypanosomes — parasites that cause lethal diseases in humans and livestock — employ an antigenic variation mechanism that involves monogenic antigen expression from a pool of >2,600 antigen-coding genes. In other eukaryotes, the expression of individual genes can be enhanced by mechanisms involving the juxtaposition of otherwise distal chromosomal loci in the three-dimensional nuclear space. However, trypanosomes lack classical enhancer sequences or regulated transcription initiation. In this context, it has remained unclear how genome architecture contributes to monogenic transcription elongation and transcript processing. Here, we show that the single expressed antigen-coding gene displays a specific inter-chromosomal interaction with a major messenger RNA splicing locus. Chromosome conformation capture (Hi-C) revealed a dynamic reconfiguration of this inter-chromosomal interaction upon activation of another antigen. Super-resolution microscopy showed the interaction to be heritable and splicing dependent. We found a specific association of the two genomic loci with the antigen exclusion complex, whereby VSG exclusion 1 (VEX1) occupied the splicing locus and VEX2 occupied the antigen-coding locus. Following VEX2 depletion, loss of monogenic antigen expres- sion was accompanied by increased interactions between previously silent antigen genes and the splicing locus. Our results reveal a mechanism to ensure monogenic expression, where antigen transcription and messenger RNA splicing occur in a specific nuclear compartment. These findings suggest a new means of post-transcriptional gene regulation.

The work was funded by Wellcome Trust Investigator Awards to D.H. [100320/Z/12/Z], by the German Research Foundation (SI 1610/2-1 and SI 1610/3-1), the Center for Integrative Protein Science (CIPSM) and by an ERC Starting Grant (3D_Tryps 715466). The University of Dundee Imaging Facility is supported by the MRC Next Generation Optical Microscopy award [MR/K015869/1]. L.S.M.M. was supported by a grant of the German Excellence Initiative to the Graduate School of Life Science, University of Würzburg.