Transcriptome profiling on G-quadruplex ligand-treated malaria parasites

In the malaria parasite AT-rich genome, the presence of G-quadruplex (G4) DNA motifs close to var gene family responsible for antigenic variation points towards the putative regulatory roles of G4 in gene expression and genome stability. However, the function of G4 in the genome biology of Plasmodium falciparum, the deadliest human malaria parasite, remains poorly understood. Here, we carried out a genome-wide survey of G4 DNA motifs using G4Hunter, which allows to search for any G4 forming sequences considering their G-richness and G-skewness, in the genome of P. falciparum. We show an enrichment of G4 DNA motifs in nucleosome-depleted regions and in the first exon of var genes, a pattern that is conserved among closely related Plasmodium species. Our results reveal a significant association of G4 with recombination breakpoints. In addition, we characterize a new G4 motif that form highly stable G4 structure and is located in the promoter of var genes. This G4 motif modulates reporter gene expression in the presence of pyridostatin (PDS). Transcriptome profiling of PDS-treated parasites show a genome-wide gene expression deregulation with 60% of G4-containing genes altered and an increase of var expression. Our results provide new evidence that G4 plays a regulatory role in gene expression of Plasmodium and in var gene recombination.