Isebe, T. | Search bioRxiv

bioRxiv2025

Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes

Genome three-dimensional organization is essential for the coordination of eukaryote gene expression. The chromosomes of the pathogen Trypanosoma brucei contain hundreds of silent variant surface glycoprotein (VSGs) genes in subtelomeric regions. However, T. brucei transcribes a single VSG gene and periodically changes the VSG expressed by transcriptional or recombination mechanisms, altering its surface coat to escape host antibodies by antigenic variation. We show that VSG-rich silent subtelomeric regions form distinct chromosome compartments from transcribed regions, with subtelomeric compartments of different chromosomes co-interacting. We uncovered chromatin-associating factors at the boundaries of transcribed and silent compartments. Among these, repressor activator-protein 1 (RAP1) marks the compartment boundaries and spreads over silent regions. Inactivation of phosphatidylinositol phosphate 5-phosphatase removed RAP1 from compartment boundaries and subtelomeric regions, disrupting compartment assembly and derepressing all VSG genes. The data show spatial segregation of repressed from transcribed chromatin and phosphoinositides regulation of silent compartment assembly and genome organization.

microbiology↗

bioRxiv2023

A PI(3,4,5)P3-dependent allosteric switch controls antigenic variation in trypanosomes

African trypanosomes evade host immune clearance by antigenic variation, causing persistent infections in humans and animals. These parasites express a homogeneous surface coat of variant surface glycoproteins (VSGs). They transcribe one out of hundreds of VSG genes at a time from telomeric expression sites (ESs) and periodically change the VSG expressed by transcriptional switching or recombination. The mechanisms underlying the control of VSG switching and its developmental silencing remain elusive. We report that telomeric ES activation and silencing entail an on/off genetic switch controlled by a nuclear phosphoinositide signaling system. This system includes a nuclear phosphatidylinositol 5-phosphatase (PIP5Pase), its substrate PI(3,4,5)P3, and the repressor-activator protein 1 (RAP1). RAP1 binds to ES sequences flanking VSG genes via its DNA binding domains and represses VSG transcription. In contrast, PI(3,4,5)P3 binds to the N-terminus of RAP1 and controls its DNA binding activity. Transient inactivation of PIP5Pase results in the accumulation of nuclear PI(3,4,5)P3, which binds RAP1 and displaces it from ESs, activating transcription of silent ESs and VSG switching. The system is also required for the developmental silencing of VSG genes. The data provides a mechanism controlling reversible telomere silencing essential for the periodic switching in VSG expression and its developmental regulation.

microbiology↗