The genetic landscape of origins of replication in P. falciparum
A variety of origin mapping approaches have enabled genome-wide identification of origins of replication (ORI) in model organisms, but only a few of studies have focused on divergent organisms. By employing three complementary approaches we provide a high-resolution map of ORIs in Plasmodium falciparum, the deadliest human malaria parasite. We profiled the distribution of ORC binding sites by ChIP-seq of two subunits and mapped active ORIs using NFS and SNS-seq. We show that ORIs lack sequence specificity but are not randomly distributed, and group in clusters. Licensing is biased towards regions of higher GC content and associated with G-quadruplex forming sequences (G4FS). While strong transcription likely enhances origin firing, active origins are depleted from transcription start sites. Instead, most accumulate in transcriptionally active gene bodies. Single molecule analysis of nanopore reads containing multiple initiation events, which could have only come from individual replicating nuclei, showed a relationship between the pace at which replication forks travel and the distance to the nearest origin.
While some similarities were drawn with the canonic eukaryote model, the distribution of ORIs in P. falciparum is likely shaped by unique genomic features such as extreme AT-richness – a product of evolutionary pressure imposed by the parasitic lifestyle.