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Totañes FIG, Gockel J, Chapman SE, Bártfai R, Boemo MA, Merrick CJ. A genome-wide map of DNA replication at single-molecule resolution in the malaria parasite Plasmodium falciparum. Nucleic Acids Res 2023; 51:2709-2724. [PMID: 36808528 PMCID: PMC10085703 DOI: 10.1093/nar/gkad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
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 ∼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.
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Affiliation(s)
| | - Jonas Gockel
- Department of Molecular Biology, Radboud University, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
| | - Sarah E Chapman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
| | - Michael A Boemo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Catherine J Merrick
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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Shaikh N, Mazzagatti A, De Angelis S, Johnson SC, Bakker B, Spierings DCJ, Wardenaar R, Maniati E, Wang J, Boemo MA, Foijer F, McClelland SE. Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses. Genome Biol 2022; 23:223. [PMID: 36266663 PMCID: PMC9583511 DOI: 10.1186/s13059-022-02781-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How replication stress and genomic instability are connected is not known. Aphidicolin-induced replication stress induces breakages at common fragile sites, but the exact causes of fragility are debated, and acute genomic consequences of replication stress are not fully explored. RESULTS We characterize DNA copy number alterations (CNAs) in single, diploid non-transformed cells, caused by one cell cycle in the presence of either aphidicolin or hydroxyurea. Multiple types of CNAs are generated, associated with different genomic regions and features, and observed copy number landscapes are distinct between aphidicolin and hydroxyurea-induced replication stress. Coupling cell type-specific analysis of CNAs to gene expression and single-cell replication timing analyses pinpointed the causative large genes of the most recurrent chromosome-scale CNAs in aphidicolin. These are clustered on chromosome 7 in RPE1 epithelial cells but chromosome 1 in BJ fibroblasts. Chromosome arm level CNAs also generate acentric lagging chromatin and micronuclei containing these chromosomes. CONCLUSIONS Chromosomal instability driven by replication stress occurs via focal CNAs and chromosome arm scale changes, with the latter confined to a very small subset of chromosome regions, potentially heavily skewing cancer genome evolution. Different inducers of replication stress lead to distinctive CNA landscapes providing the opportunity to derive copy number signatures of specific replication stress mechanisms. Single-cell CNA analysis thus reveals the impact of replication stress on the genome, providing insights into the molecular mechanisms which fuel chromosomal instability in cancer.
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Affiliation(s)
- Nadeem Shaikh
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alice Mazzagatti
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Simone De Angelis
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sarah C Johnson
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
- Current address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael A Boemo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Sarah E McClelland
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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Abstract
Background Measuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can be used as a therapeutic target for diseases like cancer. In recent years, the detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method to supersede existing single-molecule methods such as DNA fibre analysis: ONT sequencing yields long reads with high throughput, and sequenced molecules can be mapped to the genome using standard sequence alignment software. Results This paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-nucleotide resolution. DNAscent v2 also comes equipped with an autoencoder that interprets the pattern of BrdU incorporation on each ONT-sequenced molecule into replication fork direction to call the location of replication origins termination sites. DNAscent v2 surpasses previous versions of DNAscent in BrdU calling accuracy, origin calling accuracy, speed, and versatility across different experimental protocols. Unlike NanoMod, DNAscent v2 positively identifies BrdU without the need for sequencing unmodified DNA. Unlike RepNano, DNAscent v2 calls BrdU with single-nucleotide resolution and detects more origins than RepNano from the same sequencing data. DNAscent v2 is open-source and available at https://github.com/MBoemo/DNAscent. Conclusions This paper shows that DNAscent v2 is the new state-of-the-art in the high-throughput, single-molecule detection of replication fork dynamics. These improvements in DNAscent v2 mark an important step towards measuring DNA replication dynamics in large genomes with single-molecule resolution. Looking forward, the increase in accuracy in single-nucleotide resolution BrdU calls will also allow DNAscent v2 to branch out into other areas of genome stability research, particularly the detection of DNA repair. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-07736-6).
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Affiliation(s)
- Michael A Boemo
- Department of Pathology, University of Cambridge, Cambridge, UK.
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Aydogan MG, Steinacker TL, Mofatteh M, Wilmott ZM, Zhou FY, Gartenmann L, Wainman A, Saurya S, Novak ZA, Wong SS, Goriely A, Boemo MA, Raff JW. An Autonomous Oscillation Times and Executes Centriole Biogenesis. Cell 2020; 181:1566-1581.e27. [PMID: 32531200 PMCID: PMC7327525 DOI: 10.1016/j.cell.2020.05.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/19/2019] [Accepted: 05/08/2020] [Indexed: 01/18/2023]
Abstract
The accurate timing and execution of organelle biogenesis is crucial for cell physiology. Centriole biogenesis is regulated by Polo-like kinase 4 (Plk4) and initiates in S-phase when a daughter centriole grows from the side of a pre-existing mother. Here, we show that a Plk4 oscillation at the base of the growing centriole initiates and times centriole biogenesis to ensure that centrioles grow at the right time and to the right size. The Plk4 oscillation is normally entrained to the cell-cycle oscillator but can run autonomously of it-potentially explaining why centrioles can duplicate independently of cell-cycle progression. Mathematical modeling indicates that the Plk4 oscillation can be generated by a time-delayed negative feedback loop in which Plk4 inactivates the interaction with its centriolar receptor through multiple rounds of phosphorylation. We hypothesize that similar organelle-specific oscillations could regulate the timing and execution of organelle biogenesis more generally.
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Affiliation(s)
- Mustafa G Aydogan
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
| | - Thomas L Steinacker
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Mohammad Mofatteh
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Zachary M Wilmott
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Felix Y Zhou
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, UK
| | - Lisa Gartenmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Alan Wainman
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Saroj Saurya
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Zsofia A Novak
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Siu-Shing Wong
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Alain Goriely
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Michael A Boemo
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
| | - Jordan W Raff
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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Boemo MA, Cardelli L, Nieduszynski CA. The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems. PLoS Comput Biol 2020; 16:e1007651. [PMID: 32150540 PMCID: PMC7082070 DOI: 10.1371/journal.pcbi.1007651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 03/19/2020] [Accepted: 01/10/2020] [Indexed: 01/08/2023] Open
Abstract
Biological systems are made up of components that change their actions (and interactions) over time and coordinate with other components nearby. Together with a large state space, the complexity of this behaviour can make it difficult to create concise mathematical models that can be easily extended or modified. This paper introduces the Beacon Calculus, a process algebra designed to simplify the task of modelling interacting biological components. Its breadth is demonstrated by creating models of DNA replication dynamics, the gene expression dynamics in response to DNA methylation damage, and a multisite phosphorylation switch. The flexibility of these models is shown by adapting the DNA replication model to further include two topics of interest from the literature: cooperative origin firing and replication fork barriers. The Beacon Calculus is supported with the open-source simulator bcs (https://github.com/MBoemo/bcs.git) to allow users to develop and simulate their own models. Simulating a model of a biological system can suggest ideas for future experiments and help ensure that conclusions about a mechanism are consistent with data. The Beacon Calculus is a new language that makes modelling simple by allowing users to simulate a biological system in only a few lines of code. This simplicity is critical as it allows users the freedom to come up with new ideas and rapidly test them. Models written in the Beacon Calculus are also easy to modify and extend, allowing users to add new features to the model or incorporate it into a larger biological system. We demonstrate the breadth of applications in this paper by applying the Beacon Calculus to DNA replication and DNA damage repair, both of which have implications for genome stability and cancer. We also apply it to multisite phosphorylation, which is important for cellular signalling. To enable users to create their own models, we created the open-source Beacon Calculus simulator bcs (https://github.com/MBoemo/bcs.git) which is easy to install and is well-supported by documentation and examples.
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Affiliation(s)
- Michael A. Boemo
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Luca Cardelli
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
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Boemo MA, Byrne HM. Mathematical modelling of a hypoxia-regulated oncolytic virus delivered by tumour-associated macrophages. J Theor Biol 2018; 461:102-116. [PMID: 30359572 PMCID: PMC6269600 DOI: 10.1016/j.jtbi.2018.10.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/02/2018] [Accepted: 10/22/2018] [Indexed: 01/16/2023]
Abstract
A continuum model of macrophages releasing an oncolytic virus within a tumour spheroid. Predictive modelling of this treatment given in combination with radiotherapy. Investigation into how radiotherapy and oncolytic virotherapy should be scheduled.
Tumour hypoxia has long presented a challenge for cancer therapy: Poor vascularisation in hypoxic regions hinders both the delivery of chemotherapeutic agents and the response to radiotherapy, and hypoxic cancer cells that survive treatment can trigger tumour regrowth after treatment has ended. Tumour-associated macrophages are attractive vehicles for drug delivery because they localise in hypoxic areas of the tumour. In this paper, we derive a mathematical model for the infiltration of an in vitro tumour spheroid by macrophages that have been engineered to release an oncolytic adenovirus under hypoxic conditions. We use this model to predict the efficacy of treatment schedules in which radiotherapy and the engineered macrophages are given in combination. Our work suggests that engineered macrophages should be introduced immediately after radiotherapy for maximum treatment efficacy. Our model provides a framework that may guide future experiments to determine how multiple rounds of radiotherapy and macrophage virotherapy should be coordinated to maximise therapeutic responses.
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Affiliation(s)
- Michael A Boemo
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom.
| | - Helen M Byrne
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford, OX2 6GG, United Kingdom.
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Abstract
Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous-time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it. We conclude by introducing example mechanisms that can implement such circuits experimentally and discuss their individual strengths and weaknesses.
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Affiliation(s)
- Michael A. Boemo
- Department
of Physics, University of Oxford, Oxford OX1 2JD, U.K
| | | | | | - Luca Cardelli
- Department
of Computer Science, University of Oxford, Oxford OX1 2JD, U.K
- Microsoft Research Cambridge, Cambridge CB1 2FB, U.K
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