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The variant surface glycoprotein (VSG) of African trypanosomes plays an essential role in protecting the parasites from host immune factors. These trypanosomes undergo antigenic variation resulting in the expression of a single VSG isoform out of a repertoire of around 2000 genes. The molecular mechanism central to the expression and regulation of the VSG is however not fully understood.
Gene expression in trypanosomes is unusual due to the absence of typical RNA polymerase II promoters and the polycistronic transcription of genes. The regulation of gene expression is therefore mainly post-transcriptional. Regulatory sequences, mostly present in the 3´ UTRs, often serve as key elements in the modulation of the levels of individual mRNAs. In T. brucei VSG genes, a 100 % conserved 16mer motif within the 3´ UTR has been shown to modulate the stability of VSG transcripts and hence their expression. As a stability-associated sequence element, the absence of nucleotide substitutions in the motif is however unusual. It was therefore hypothesised that the motif is involved in other essential roles/processes besides stability of the VSG transcripts.
In this study, it was demonstrated that the 100 % conservation of the 16mer motif is not essential for cell viability or for the maintenance of functional VSG protein levels. It was further shown that the intact motif in the active VSG 3´ UTR is neither required to promote VSG silencing during switching nor is it needed during differentiation from bloodstream forms to procyclic forms. Crosstalk between the VSG and procyclin genes during differentiation to the insect vector stage is also unaffected in cells with a mutated 16mer motif. Ectopic overexpression of a second VSG however requires the intact motif to trigger silencing and exchange of the active VSG, suggesting a role for the motif in transcriptional VSG switching. The 16mer motif therefore plays a dual role in VSG in situ switching and stability of VSG transcripts. The additional role of the 16mer in the essential process of antigenic variation appears to be the driving force for the 100 % conservation of this RNA motif.
A screen aimed at identifying candidate RNA-binding proteins interacting with the 16mer motif, led to the identification of a DExD/H box protein, Hel66. Although the protein did not appear to have a direct link to the 16mer regulation of VSG expression, the DExD/H family of proteins are important players in the process of ribosome biogenesis. This process is relatively understudied in trypanosomes and so this candidate was singled out for detailed characterisation, given that the 16mer story had reached a natural end point. Ribosome biogenesis is a major cellular process in eukaryotes involving ribosomal RNA, ribosomal proteins and several non-ribosomal trans-acting protein factors. The DExD/H box proteins are the most important trans-acting protein factors involved in the biosynthesis of ribosomes. Several DExD/H box proteins have been directly implicated in this process in yeast. In trypanosomes, very few of this family of proteins have been characterised and therefore little is known about the specific roles they play in RNA metabolism. Here, it was shown that Hel66 is involved in rRNA processing during ribosome biogenesis. Hel66 localises to the nucleolus and depleting the protein led to a severe growth defect. Loss of the protein also resulted in a reduced rate of global translation and accumulation of rRNA processing intermediates of both the small and large ribosomal subunits. Hel66 is therefore an essential nucleolar DExD/H protein involved in rRNA processing during ribosome biogenesis. As very few protein factors involved in the processing of rRNAs have been described in trypanosomes, this finding represents an important platform for future investigation of this topic.
Antigenic variation of surface proteins is a commonly used strategy among pathogens to evade the host immune response [63]. The mechanism underlying antigenic variation relies on monoallelic exclusion of a single gene from a hypervariable multigene family combined with repeated, systematic changes in antigen expression. In many systems, these gene families are arranged in subtelomeric contingency loci that are subject to both transcriptional repression and enhanced mutagenesis and recombination [16].
Eviction of a selected gene from a repressed antigen repertoire can be achieved e.g. by recombination into a dedicated, transcriptionally permissive site or by local epigenetic alterations in chromatin composition of the selected gene.
Both processes are ultimately affected by genome architecture. Architectural proteins controlling antigenic variation have, however, remained elusive in any pathogen.
The unicellular protozoan parasite Trypanosoma brucei evades the host immune response by periodically changing expression of a single variant surface glycoprotein (VSG) from a repertoire of ~3000 VSG genes – the largest mutually exclusively expressed gene family described today. To activate a selected VSG gene, it needs to be located in a dedicated expression site that becomes subject to relocation into a distinct, transcriptionally active subnuclear compartment, the expression site body (ESB). Whereas this emphasizes the importance of nuclear architecture in regulating antigen expression in T. brucei, the mechanisms underlying spatial positioning of DNA in T. brucei are not well understood.
In this study I applied genome-wide chromosome conformation capture (Hi-C) to obtain a comprehensive picture of the T. brucei genome in three dimensions, both in procyclic and bloodstream form parasites. Hi-C revealed a highly structured nucleus with megabase chromosomes occupying distinct chromosome territories. Further, specific trans interactions between chromosomes, among which are clusters of centromeres, rRNA genes and procyclins became apparent. With respect to antigenic variation, Hi-C revealed a striking compaction of the subtelomeric VSG gene repertoire and a strong clustering of transcriptionally repressed VSG-containing expression sites. Further, Hi-C analyses confirmed the spatial separation of the actively transcribed from the silenced expression sites in three dimensions.
I further sought to characterize architectural proteins mediating nuclear architecture in T. brucei. Whereas CTCF is absent in non-metazoans, we found cohesin to be expressed throughout the cell cycle, emphasizing a function beyond sister chromatid cohesion in S-phase.
By Chromatin-Immunoprecipitation with sequencing (ChIPseq), I found cohesin enrichment to coincide with the presence of histone H3 vari- ant (H3.V) and H4 variant (H4.V). Most importantly, cohesin and the histone variants were enriched towards the VSG gene at silent and active expression sites.
While the deletion of H3.V led to increased clustering of expression sites in three dimensions and increased chromatin accessibility at expression site promoters, the additional deletion of H4.V increased chromatin accessibility at expression sits even further.
RNAseq showed that mutually exclusive VSG expression was lost in H3.V and H4.V single and double deletion mutants. Immunofluorescence imaging of surface VSGs, flow cytometry and single-cell RNAseq revealed a progressive loss of VSG-2 expression, indicative of an increase in VSG switching rate in the H3.V/H4.V double deletion mutants. Using long-read sequencing technology, we found that VSG switching occurred via recombination and concluded, that the concomitant increase in spatial proximity and accessibility among expression sites facilitated the recombination event.
I therefore identified the histone variants H3.V and H4.V to act at the interface of global nuclear architecture and chromatin accessibility and to represent a link between genome architecture and antigenic variation.