Discussion

Nucleic acids (DNA and RNA) can form several different secondary structures and these can influence general gene expression. Among these structures, one that has recently gained the spotlight is the G-quadruplex (G4). G4s are formed by the stacking of guanine quartets and they have well-established roles at the DNA level in controlling gene expression, genome stability and telomere maintenance.  ‘rG4s’ have recently been identified at the RNA level in several model systems including human cells. G4 structures have been identified by our group and others at the DNA level in Plasmodium falciparum using bio-informatics algorithms and structure-specific antibodies. In view of the important A/T bias of this parasite genome, the presence of such G-rich motifs might indicate that they are maintained in the genome to play specific regulatory roles.  This is particularly intriguing because almost half of the predicted G4 motifs in the genome are associated with the major virulence gene family var. The var genes are a group of nearly 60 genes coding for the Pfemp1 protein that is involved in immune evasion and malaria pathogenicity. Interestingly, only one var gene is express at the time while the others are silenced. The presence of G4 motifs in the neighborhood of these genes could be one of the keys to understand the fine regulation of this family. Building upon our work on DNA G4s, we have now identified putative G4 structures at the RNA level in Plasmodium falciparum. This was achieved by structure-specific sequencing of the transcriptome using a technique called rG4-seq.  Among the genes with rG4s, genes encoding DNA binding proteins, as well as var virulence genes, are over-represented. We decided to investigate the influence of these rG4s on gene expression at the RNA and protein levels. For this, we are focusing on several different rG4-containing genes, including var genes and the gene encoding histone H4. By treating parasites with a drug, carboxypyridostatin (cPDS), that targets and specifically stabilizes rG4 structures we are able to observe an influence of these structures on the studied genes in presence of the drug. We believe that rG4s may play a role in gene expression at both RNA and protein levels. Further studies involving reporter genes are planned to better investigate their role.