Epigenetically-regulated RNA-binding proteins signify malaria hypnozoite dormancy

SUMMARYDormancy enables relapsing malaria parasites, such as Plasmodium vivax and cynomolgi, to survive unfavorable conditions and maximize chances for transmission. It is caused by hypnozoites, parasites remaining quiescent inside hepatocytes before reactivating and establishing blood-stage infection. We integrated various omics approaches to explore gene-regulatory mechanisms underlying hypnozoite formation and reactivation. Genome-wide profiling of epigenetic marks identified a small set of genes that gets epigenetically silenced during hepatic infection of relapsing parasites. Furthermore, by combining single-cell transcriptomics, chromatin accessibility profiling and fluorescent in situ RNA hybridization, we show that these genes are exclusively expressed in hypnozoites and their silencing precedes parasite development. Intriguingly, these hypnozoite-specific genes mainly encode proteins with RNA-binding domains. We, hence, propose that repressive RNA-binding proteins keep hypnozoites in a developmentally competent but dormant state and heterochromatin-mediated silencing of the corresponding genes enables hypnozoite reactivation. Further testing of this hypothesis could provide clues for targeted reactivation and killing of these vicious pathogens.