Discussion

Malaria parasites have evolved mechanisms to enable them to avoid their host’s immune response and maintain an infection that is sufficiently persistent to allow efficient transmission to their mosquito vector. This is largely accomplished through antigenic variation, the systematic alteration of surface proteins exposed to the immune system. The parasite’s genome contains large, multicopy gene families, with each individual gene encoding an antigenically distinct form of the surface protein. By systematically activating and silencing individual genes, the parasites can alter their antigenic signature and thus avoid antibodies produced by the host directed toward these surface antigens. This process is remarkably effective, with infections typically able to persist for over a year. For P. falciparum, the gene family encoding the primary antigenic determinant is called var and consists of 40-90 genes per haploid genome. Current models indicate that only a single gene is expressed at any given time, with the remainder of the family maintained in a transcriptionally silent state via repressive epigenetic chromatin modifications. However, using single cell transcriptomic analysis, we have recently discovered that var gene expression is much more flexible than previously appreciated. We found that while parasites typically express a single var gene, individual parasites can also express multiple var genes simultaneously or enter a state in which little or no var gene expression is detectable. Further, by manipulating the availability of the methyl donor S-adenosyl methionine, we can completely disrupt mutually exclusive expression, leading to stable, high-level expression of several var genes in each cell. These data challenge the dogma that var gene expression is limited to a single gene at a time and shed light on the mechanisms underlying mutually exclusive expression, transcriptional switching and var gene choice.