Biology subjects

Boemo, M. A.

Publications and source records attributed to Boemo, M. A..

15 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↗

bioRxiv2026

A genome language model for mapping DNA replication origins

Origin firing is a central process during DNA replication, but specific sequences defining replication origin usage have not been defined in human cells. Here, we show that a genome language model can accurately predict which sequences can act as an origin of replication, thereby enabling the fast and cost-effective creation of genome-wide replication origin maps. We fine-tuned a genome language model on the primary sequence of mapped human origins to establish ORILINX (ORIgin of replication Language-model Inference via Nucleotide conteXt) and found that it learns a rich representation of sequence features linked to replication initiation, extending beyond known predictive features such as GC-content and G-quadruplex motifs. When applied genome-wide, the models sequence-derived origin calling closely mirrors origin efficiency inferred from replication timing, suggesting that intrinsic sequence context encodes information relevant to initiation frequency. Furthermore, we performed Short Nascent Strand sequencing (SNS-seq) and Repli-seq to demonstrate that ORILINX can generalise to other mammalian genomes, such as those of mice and sheep, as well as other vertebrates such as chickens. Finally, we packaged ORILINX into a simple, easy-to-use tool which is available at https://github.com/Pfuderer/ORILINX.git.

genomics↗

bioRxiv2025

CAD-C reveals centromere pairing and near-perfect alignment of sister chromatids

Three-dimensional (3D) genome organization plays a central role in gene regulation, chromatin folding, and genome stability. Although chromosome-conformation capture (3C)-derived methods have revolutionized our understanding of genome architecture, most remain limited in resolution, in their capacity to detect multiway interactions and in their ability to distinguish sister chromatids. Here, we present CAD-C, a new chromatin-conformation capture strategy that uses Caspase-Activated DNase (CAD) to fragment chromatin. Fragmentation of chromatin to the nucleosome level by CAD digestion substantially enhances proximity ligation, enabling formation of multi-nucleosome ligation products. Nanopore sequencing of these long DNA molecules allows reconstruction of chromatin fiber connectivity and 3D contact maps with single nucleosome resolution. Importantly, CAD-C is able to identify sister-chromatid interactions at high resolution which reveals that centromeres are closely paired and that cohesin maintains sister chromatids in near perfect alignment where the same nucleosomes are associated across sisters. Such precise alignment has significant implications for chromosome structure and the mechanisms by which cohesion is established.

genomics↗

bioRxiv2025

Stalling of elongating Pol II triggers Ser7 phosphorylation in trans to drive transcription recovery

DNA is scattered with obstacles that stall RNA polymerase II (Pol II) and block the production of full-length transcripts. Two mechanisms are known to resolve stalled Pol II: transcription-coupled nucleotide excision repair (TC-NER) and the "last resort" Pol II ubiquitylation-degradation pathway. Here, we uncover a third, distinct mechanism that alerts incoming Pol II molecules to roadblocks ahead and primes them for efficient elongation. We show that transcription stalling triggers GSK3-mediated phosphorylation of Ser7 residues (Ser7P) on the Pol II C-terminal domain. Unexpectedly, this phosphorylation occurs in trans: obstacles in gene bodies induce Ser7P on Pol II complexes at gene beginnings. This modification enables processive transcription while restraining excessive Pol II degradation by the "last resort" pathway. Our findings reveal an adaptive system that preserves transcriptional homeostasis by coordinating polymerase behavior across the gene in response to elongation stress.

molecular biology↗

bioRxiv2025

ecDNA replication is disorganised and vulnerable to replication stress

Extrachromosomal DNA (ecDNA) is a critical driver of cancer progression, contributing to tumour growth, evolution, and therapeutic resistance through oncogene amplification. Despite its significance, the replication of ecDNA remains poorly understood. In this study, we investigated the replication dynamics of ecDNA using high-resolution replication timing analysis (Repli-seq) and DNAscent, a method for measuring origin firing and replication fork movement based on ultra-long read Oxford Nanopore Sequencing, that we applied to both bulk DNA and to ecDNA isolated with FACS-based Isolation of Native ecDNA (FINE), a new method for isolating intact, chromatinised ecDNA without DNA or protein digestion. We demonstrate that ecDNA in the COLO 320DM colorectal cancer cell line exhibits largely asynchronous replication throughout the S phase, contrasting with the conserved replication timing of the corresponding normal linear chromosomal DNA in RPE-1 cells and the chromosomally reintegrated ecDNA in COLO 320HSR, which forms a homogeneously staining region. Replication origins on ecDNA are redistributed, and replication forks exhibit reduced velocity and increased stalling, particularly near the c-MYC oncogene. Under replication stress induced by hydroxyurea treatment, ecDNA replication is further compromised, leading to altered origin activation, reduced fork velocity and eventual ecDNA depletion from cells. Our findings reveal fundamental differences in the replication dynamics of ecDNA, providing insights that could inform the development of therapies targeting ecDNA-associated oncogene amplification in cancer.

cancer biology↗

bioRxiv2025

High levels of DNA replication initiation factors indicate ATR inhibitor sensitivity via excessive origin firing

Inhibitors of ATR, a central kinase controlling DNA replication origin firing and cellular checkpoint activity, are currently in multiple clinical trials, yet mechanisms underpinning sensitivity and robust patient stratification biomarkers are lacking. We used functional genomics approaches to identify molecular mechanisms driving sensitivity to the ATR inhibitor (ATRi) ceralasertib. Replication stress-associated patterns of DNA copy number alterations identified a subset of sensitive breast cancer cell lines. In parallel, we performed proteomics, phosphoproteomics and gene expression analyses and discovered that sensitive cell lines had higher expression of DNA replication origin firing factors, and massively increased origin firing in response to ATRi. ATRi sensitivity was partly rescued upon co-treatment with XL-413, a CDC7 inhibitor that decreases origin firing. High expression of replication initiation factors correlated with ATRi sensitivity across multiple cancer types, and in acute myeloid leukemia patient samples. Together, this study reveals a novel contribution of lethal origin firing capacity in determining the sensitivity of cancer cells to ATR inhibition and demonstrates the predictive potential of mechanism-specific copy number alterations, providing key steps towards developing a multimodal clinically applicable biomarker for ATR inhibitors.

cancer biology↗

bioRxiv2024

DNA replication timing reveals genome-wide features of transcription and fragility

DNA replication in humans requires precise regulation to ensure accurate genome duplication and maintain genome integrity. A key indicator of this regulation is replication timing, which reflects the interplay between origin firing and fork dynamics. We present a high-resolution (1-kilobase) mathematical model that maps firing rate distributions to replication timing profiles across various cell lines, validated using Repli-seq data. The model effectively captures genome-wide replication patterns while identifying local discrepancies. Notably, regions where the model and data diverge often overlap with fragile sites and long genes, highlighting the influence of genomic architecture on replication dynamics. Conversely, regions of high concordance are associated with open chromatin and active promoters, where elevated firing rates facilitate timely fork progression and reduce replication stress. By establishing these correlations, our model provides a valuable framework for exploring the structural interplay between replication timing, transcription, and chromatin organisation, offering new insights into mechanisms underlying replication stress and its implications for genome stability and disease.

systems biology↗

bioRxiv2024

Regulation of replication timing in Saccharomyces cerevisiae

In order to maintain genomic integrity, DNA replication must be highly coordinated. Disruptions in this process can cause replication stress which is aberrant in many pathologies including cancer. Despite this, little is known about the mechanisms governing the temporal regulation of DNA replication initiation, thought to be related to the limited copy number of firing factors. Here, we present a high (1-kilobase) resolution stochastic model of Saccharomyces cerevisiae whole-genome replication in which origins compete to associate with limited firing factors. After developing an algorithm to fit this model to replication timing data, we validated the model by reproducing experimental inter-origin distances, origin efficiencies, and replication fork directionality. This suggests the model accurately simulates the aspects of DNA replication most important for determining its dynamics. We also use the model to predict measures of DNA replication dynamics which are yet to be determined experimentally and investigate the potential impacts of variations in firing factor concentrations on DNA replication.

systems biology↗

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

A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells

DNA replication stress is a hallmark of cancer that is exploited by chemotherapies. Current assays for replication stress have low throughput and poor resolution whilst being unable to map the movement of replication forks genome-wide. We present a new method that uses nanopore sequencing and artificial intelligence to map forks and measure their rates of movement and stalling in melanoma and colon cancer cells treated with chemotherapies. Our method can differentiate between fork slowing and fork stalling in cells treated with hydroxyurea, as well as inhibitors of ATR, WEE1, and PARP1. These different therapies yield different characteristic signatures of replication stress. We assess the role of the intra-S-phase checkpoint on fork slowing and stalling and show that replication stress dynamically changes over S-phase. This method requires sequencing on only a single nanopore flow cell, and the cost-effectiveness and high throughput enables functional screens to determine how human cancers respond to replication-targeted therapies.

cancer biology↗

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

DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning

The detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method for the high-throughput measurement of DNA replication dynamics with single-molecule resolution. This paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-base resolution. DNAscent v2 comes equipped with an autoencoder that detects replication forks, origins, and termination sites in ONT sequencing reads from both synchronous and asynchronous cell populations, outcompeting previous versions and other tools across different experimental protocols. DNAscent v2 is open-source and available at https://github.com/MBoemo/DNAscent.

bioinformatics↗

bioRxiv2019

The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems

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. Author summarySimulating 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.

systems biology↗

bioRxiv2019

A free-running oscillator times and executes centriole biogenesis

The accurate timing of organelle biogenesis and the precise regulation of organelle size are crucial for cell physiology. Centriole biogenesis initiates exclusively in S-phase, when a daughter centriole emerges from the side of a pre-existing mother and grows until it reaches its mothers size. This process is regulated by Polo-like kinase 4 (Plk4), which is recruited to centrioles in oscillatory waves in flies and human cells 1,2. The nature and function of Plk4 oscillations is, however, unknown. Here we discover that Plk4 forms an adaptive oscillator at the base of the growing centriole, whose function is to time and set the duration of centriole biogenesis in Drosophila embryos. We demonstrate that the Plk4 oscillator is free-running of, but is entrained and calibrated by, the core Cdk/Cyclin cell-cycle oscillator, explaining how centrioles can duplicate independently of the cell cycle 3-5. Mathematical modelling and further experiments indicate that the Plk4 oscillator is generated by a time-delayed negative-feedback loop in which Plk4 recruitment to, and dissociation from, the centriole is monitored via changes in the affinity-state of its centriolar receptor, Asterless. We postulate that such organelle-specific autonomous oscillators could regulate the timing and execution of organelle biogenesis more generally.

cell biology↗

bioRxiv2018

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

The replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We now report a sequencing method for the measurement of replication fork movement on single molecules by Detecting Nucleotide Analogue signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect BrdU incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse labelling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kb, to generate the first whole genome single-molecule map of DNA replication dynamics and discover a new class of low frequency stochastic origins in budding yeast.

genomics↗