DNA helicase RecQ1 regulates expression of virulence genes in Plasmodium falciparum via heterochromatin alteration. Plasmodium falciparum

Plasmodium falciparum var gene family encodes ~60 surface antigens that contribute to the major pathogenesis in severe malaria. Mutually exclusive expression of individual var genes is an immune evasion mechanism by which P. falciparum escapes the host immune responses. In this study, we determined the roles of two RecQ DNA helicase family members, PfRecQ1 and PfWRN, in regulation of gene expression in P. falciparum. Through genetic manipulation, we found that the complete var repertoire was silenced upon PfRecQ1 knockout, whereas their expression did not show noticeable changes when PfWRN was knocked out. Additionally, knocking out either of these two helicases changed the perinuclear cluster distribution of subtelomeres and subtelomeric var genes. Deletion of PfRecQ1 did not result in changes of the global distribution of the heterochromatin mark trimethylated H3K9 (H3K9me3) over gene bodies including those for the var genes, whereas it led to an increase of H3K9me3 at the transcription start site (TSS) of upsC1 var gene when this gene became silent upon PfRecQ1 deletion. ChIP-seq assay showed that PfRecQ1 was enriched globally at the TSSs of all genes. In contrast, PfWRN-enriched regions were seen at the gene bodies of the var gene family, but not of non-var genes or at TSSs of all genes. In agreement with the transcriptome analysis, upon PfRecQ1 deletion, upsC1 var gene moved from the active perinuclear transcription region to a silenced region of the upsC type. These findings highlight that the PfRecQ1 protein is essential for the transcription maintenance of var genes.