Biology subjects

Chapman, S. E.

Publications and source records attributed to Chapman, S. E..

4 recordsLinked to original sources

bioRxiv2026

Nanopore sequencing reveals the DNA replication timing programme of the malaria parasite Plasmodium falciparum

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.

genomics↗

bioRxiv2024

DNA replication dynamics are associated with genome composition in Plasmodium species

Plasmodium species have variable genome compositions: many have an A/T-content of at least 80% while others are similar in composition to human cells. Here, we made a direct comparison of DNA replication dynamics in two Plasmodium species whose genomes differ by [~]20% A/T-content. This yielded fundamental insights into how DNA composition may affect replication. The highly A/T-biased genome of P. falciparum showed unusual replication dynamics that were not observed in the more balanced P. knowlesi - which had dynamics more like those of human cell lines. We observed that replication forks moved 50% slower in P. falciparum than in P. knowlesi. In P. falciparum, replication forks slowed down over the course of S-phase whereas in P. knowlesi, fork speed increased as in human cells. Furthermore, in both P. knowlesi and human cells, replication forks were strikingly slowed by sequences of particularly high A/T-bias, but in P. falciparum, although replication forks were inherently slow, they were not particularly slow in such biased sequences. Thus, the replisome of P. falciparum may have evolved alongside its extremely biased genome, making it unusually robust to sequence bias. Since several antimalarial drugs act to stall DNA replication, this study may have implications for the effectiveness of, and development of, antimalarial therapies.

microbiology↗

bioRxiv2022

Replication origin mapping in the malaria parasite Plasmodium falciparum

The malaria parasite Plasmodium falciparum replicates via schizogony: a fundamentally unusual type of cell cycle involving asynchronous replication of multiple nuclei within the same cytoplasm. It also has one of the most A/T-biased genomes ever sequenced. Here, we present the first comprehensive study of the specification and activation of DNA replication origins during Plasmodium schizogony. Potential replication origins were found to be abundant, with ORC1-binding sites detected every [~]800 bp throughout the genome. They had no motif enrichment, but were biased towards areas of higher G/C content. Origin activation was then measured at single-molecule resolution via new DNAscent technology that measures fork movement by detecting base analogues BrdU and EdU in DNA sequenced on the Oxford nanopore platform (https://github.com/MBoemo/DNAscent). DNAscent-called origins were found to be much less dense than ORC1-binding sites, with origins activated preferentially in areas of low transcriptional activity. Consistently, replication forks moved fastest through the most lowly transcribed genes, suggesting that conflicts between transcription and origin firing inhibit efficient replication, and that P. falciparum has evolved its S-phase to minimise such conflicts.

microbiology↗

bioRxiv2020

Altered skeletal muscle glucose-fatty acid flux in amyotrophic lateral sclerosis (ALS)

Amyotrophic lateral sclerosis (ALS) is characterized by the degeneration of upper and lower motor neurons, yet an increasing number of studies in both mouse models and patients with ALS suggest that altered metabolic homeostasis is a feature of disease. Pre-clinical and clinical studies have shown that modulation of energy balance can be beneficial in ALS. However, our capacity to target specific metabolic pathways or mechanisms requires detailed understanding of metabolic dysregulation in ALS. Here, using the SOD1G93A mouse model of ALS, we demonstrate that an increase in whole-body metabolism occurs at a time when glycolytic muscle exhibits an increased dependence on fatty acid oxidation. Using myotubes derived from muscle of ALS patients, we also show that increased dependence on fatty acid oxidation is associated with increased whole-body energy expenditure. In the present study, increased fatty acid oxidation was associated with slower disease progression. However, we observed considerable heterogeneity in whole-body metabolism and fuel oxidation profiles across our patient cohort. Thus, future studies that decipher specific metabolic changes at an individual patient level are essential for the development of treatments that aim to target metabolic pathways in ALS.

neuroscience↗