A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite Plasmodium falciparum

The malaria parasite Plasmodium falciparum replicates via schizogony: an unusual type of cell cycle involving asynchronous replication of multiple nuclei within the same cytoplasm. Here, we present the first comprehensive study of DNA replication origin specification and activation during Plasmodium schizogony. Potential replication origins were abundant, with ORC1-binding sites detected every similar to 800 bp. In this extremely A/T-biased genome, the sites were biased towards areas of higher G/C content, and contained no specific sequence motif. Origin activation was then measured at single-molecule resolution using newly developed DNAscent technology: a powerful method of detecting replication fork movement via base analogues in DNA sequenced on the Oxford Nanopore platform. Unusually, origins were preferentially activated in areas of low transcriptional activity, and replication forks also moved fastest through lowly transcribed genes. This contrasts with the way that origin activation is organised in other systems, such as human cells, and suggests that P. falciparum has evolved its S-phase specifically to minimise conflicts between transcription and origin firing. This may be particularly important to maximise the efficiency and accuracy of schizogony, with its multiple rounds of DNA replication and its absence of canonical cell-cycle checkpoints.

Automated summary

This study investigates DNA replication origin specification and activation in Plasmodium schizogony, finding abundant potential replication origins biased towards areas of higher G/C content. Origin activation is preferentially observed in areas of low transcriptional activity, with replication forks moving fastest through lowly transcribed genes. These findings suggest that P. falciparum has evolved its S-phase to minimize conflicts between transcription and origin firing, which is crucial for efficient and accurate schizogony.