Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes

Genome three-dimensional organization is essential for eukaryotic gene expression. The chromosomes of the pathogen Trypanosoma brucei contain hundreds of silent variant surface glycoprotein (VSG) genes in subtelomeric regions. T. brucei transcribes a single VSG gene and periodically changes the VSG expressed, altering its surface coat to escape host antibodies by antigenic variation. We show that T. brucei core and subtelomeric chromosome compartments are separated by distinct boundaries and display topologically associating domains and loops. Chromosomes co-interact through compartment boundaries, which insulate silent subtelomeric from transcribed core compartments. We uncover chromatin-associating factors at the boundaries, including repressor-activator protein 1 (RAP1), which spreads over silent compartments. Inactivation of the RAP1 regulator, phosphatidylinositol phosphate 5-phosphatase, removes RAP1 from boundaries and subtelomeric compartments, disrupting chromatin compartment contacts and activating all VSG genes. The data show spatial segregation of repressed from transcribed chromatin and phosphoinositide regulation of compartment assembly and genome organization.