Nanopore sequencing reveals the DNA replication timing programme of the malaria parasite Plasmodium falciparum
- 1University of Cambridge
Abstract
The DNA replication timing programme, defined as the temporal order in which genomic loci replicate, is of fundamental importance to maintaining genome stability. In human cells, replication timing is routinely measured using Repli-seq which reveals that the human genome is divided into replication timing domains that replicate in early or late S-phase. These timing domains are associated with gene expression, chromatin compaction, and three-dimensional genome organisation. In particular, late-replicating domains can be hotspots of genomic instability under replication stress. Because of the parasite's unusual cell cycle, Repli-seq cannot be used in the malaria parasite Plasmodium falciparum, leaving the open question as to whether its genome is divided into replication timing domains and how this might impact evolution of the parasite. Here, we leverage the power of Oxford Nanopore Technologies long-read DNA sequencing together with DNAscent to determine, for the first time, the replication timing programme of P. falciparum. We show how it relates to elevated rates of DNA breaking and replication fork stalling, and predict that these stalls are predominantly transient.
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BibTeX
@misc{huang2026nanopore,
title = {{Nanopore sequencing reveals the DNA replication timing programme of the malaria parasite Plasmodium falciparum}},
author = {X. Huang and F. Berkemeier and R. Berners-Lee and K. Sherborne and S. E. Chapman and C. J. Merrick and M. A. Boemo},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.12.758579},
url = {https://www.biorxiv.org/content/10.64898/2026.10.12.758579v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Nanopore sequencing reveals the DNA replication timing programme of the malaria parasite Plasmodium falciparum
AU - X. Huang
AU - F. Berkemeier
AU - R. Berners-Lee
AU - K. Sherborne
AU - S. E. Chapman
AU - C. J. Merrick
AU - M. A. Boemo
PY - 2026
DA - 2026/10/12
PB - bioRxiv
DO - 10.64898/2026.10.12.758579
UR - https://www.biorxiv.org/content/10.64898/2026.10.12.758579v1
AB - The DNA replication timing programme, defined as the temporal order in which genomic loci replicate, is of fundamental importance to maintaining genome stability. In human cells, replication timing is routinely measured using Repli-seq which reveals that the human genome is divided into replication timing domains that replicate in early or late S-phase. These timing domains are associated with gene expression, chromatin compaction, and three-dimensional genome organisation. In particular, late-replicating domains can be hotspots of genomic instability under replication stress. Because of the parasite's unusual cell cycle, Repli-seq cannot be used in the malaria parasite Plasmodium falciparum, leaving the open question as to whether its genome is divided into replication timing domains and how this might impact evolution of the parasite. Here, we leverage the power of Oxford Nanopore Technologies long-read DNA sequencing together with DNAscent to determine, for the first time, the replication timing programme of P. falciparum. We show how it relates to elevated rates of DNA breaking and replication fork stalling, and predict that these stalls are predominantly transient.
ER -