DNA helicase RecQ1 regulates mutually exclusive expression of virulence genes in <i>Plasmodium falciparum</i> via heterochromatin alteration.

Abstract

The <i>Plasmodium falciparum var</i> gene family encodes ∼60 surface antigens by which parasites escape the host immune responses via clonal expression of <i>var</i> genes. However, the mechanism controlling this mutual exclusivity, associated with alterations in chromatin assembly, is not understood. Here, we determined how expression of the <i>var</i> gene family is regulated by two RecQ DNA helicase family members, PfRecQ1 and PfWRN, in <i>P. falciparum</i> Through genetic manipulation, we found that the complete <i>var</i> repertoire was silenced on <i>PfRecQ1</i> knockout, whereas their expression did not show noticeable changes when <i>PfWRN</i> was knocked out. More important, mutually exclusive expression of <i>var</i> genes could be rescued by complementation of PfRecQ1. In addition, knocking out either of these two helicase genes changed the perinuclear cluster distribution of subtelomeres and subtelomeric <i>var</i> genes. Whereas deletion of <i>PfRecQ1</i> increased the heterochromatin mark trimethylated (H3K9me3) at the transcription start site (TSS) of the <i>var</i> gene <i>upsC1</i>, that deletion had no effect on the global distribution of H3K9me3 over gene bodies, including those for the <i>var</i> genes. ChIP-seq assay showed that PfRecQ1 was enriched globally at the TSSs of all genes, whereas PfWRN-enriched regions occurred at the gene bodies of the <i>var</i> gene family, but not of other genes or at TSSs of all genes. On <i>PfRecQ1</i> deletion, the <i>upsC1 var</i> gene moved from the active perinuclear transcription region to a silenced region of the <i>upsC</i> type. These findings imply that PfRecQ1, but not PfWRN, is essential for maintaining the clonal expression of <i>var</i> genes.