Genome organization and DNA accessibility control antigenic variation in trypanosomes

Area of Science:

• Genetics
• Molecular Biology
• Parasitology

Background:

• Pathogenic organisms employ antigenic variation to evade host immune responses.
• Antigenic variation relies on large, diverse antigen gene reservoirs and regulated expression.
• Three-dimensional genome architecture and DNA accessibility influence homologous recombination and gene expression.

Purpose of the Study:

• To identify factors linking three-dimensional genome architecture, chromatin conformation, and antigenic variation.
• To overcome challenges in assembling repetitive antigen-gene arrays in pathogens like Trypanosoma brucei.

Main Methods:

• De novo haplotype-specific assembly of antigen-gene arrays using long-read sequencing.
• Genome-wide chromosome conformation capture (Hi-C) to analyze genome partitioning.
• Fluorescence in situ hybridization, ATAC-seq, and single-cell RNA sequencing to assess chromatin and gene expression.
• Investigating the role of histone variants H3.V and H4.V.

Main Results:

• Antigen-encoding subtelomeric regions in Trypanosoma brucei are organized into distinct, compact compartments.
• Deletion of histone variants H3.V and H4.V promotes antigen-gene clustering and increases DNA accessibility.
• Histone variant deletion enhances antigen expression switching via homologous recombination.

Conclusions:

• Histone variants H3.V and H4.V act as a molecular link between genome architecture, chromatin conformation, and antigenic variation.
• This finding provides novel insights into the regulation of immune evasion strategies in pathogens.