17 papers · ranked by Valyu relevance
Razie Yousefi, Maga Rowicka
Eukaryotic DNA replication is elaborately orchestrated to duplicate the genome timely and faithfully. Replication initiates at multiple origins from which replication forks emanate and travel bi-directionally. The complex spatio-temporal regulation of DNA replication remains incompletely understood. To study it…
Bertrand Theulot, Laurent Lacroix, Jean-Michel Arbona, Gael A. Millot + 10 more
'Gael A. Millot' 'Etienne Jean' 'Corinne Cruaud' 'Jade Pellet' 'Florence Proux' 'Magali Hennion' 'Stefan Engelen' 'Arnaud Lemainque' 'Benjamin Audit' 'Olivier Hyrien' 'Benoît Le Tallec'] Little is known about replication fork velocity variations along eukaryotic genomes, since reference techniques to determine fork…
Razie Yousefi, Maga Rowicka, Dominik Wodarz
Eukaryotic DNA replication is elaborately orchestrated to duplicate the genome timely and faithfully. Replication initiates at multiple origins from which replication forks emanate and travel bi-directionally. The complex spatio-temporal regulation of DNA replication remains incompletely understood. To study it…
Ghanendra Singh
Replication fork progression complex plays an essential role during DNA replication. It travels along with the DNA with a particular speed called replication fork speed. Faithful duplication of the genome requires strict control over replication fork speed. Both acceleration and pausing mechanisms of the replication…
Guillaume Guilbaud, Aurélien Rappailles, Antoine Baker, Chun-Long Chen + 7 more
'Chun-Long Chen' 'Alain Arneodo' 'Arach Goldar' "Yves d'Aubenton-Carafa" 'Claude Thermes' 'Benjamin Audit' 'Olivier Hyrien' 'Christopher E. Pearson'] Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large…
Chinmaya Pradhan, Bhakti Mehta, Nirjharini Saha, Mrinal Srivastava + 1 more
Eukaryotic DNA replication must remain robust under thermal, chemical, and genotoxic stress despite large fluctuations in replication dynamics. Here, we develop a lattice-based stochastic Monte Carlo framework for whole-genome replication in Saccharomyces cerevisiae at single base-pair resolution, incorporating…
Maria Anna Rapsomaniki, Stella Maxouri, Manuel Ramirez Garrastacho, Patroula Nathanailidou + 4 more
DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication…
Francis Isidore Garcia Totañes, Sarah E. Chapman, Subash Kumar Rai, Mathew J. K. Jones + 2 more
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…
Francis Isidore Garcia Totañes, Sarah E Chapman, Subash Kumar Rai, Mathew J K Jones + 2 more
'Subash\xa0Kumar Rai' 'Mathew\xa0J K Jones' 'Michael\xa0A Boemo' 'Catherine\xa0J Merrick'] Title: Abstract Plasmodium species have variable genome compositions: many have an A/T content >80%, while others are similar in composition to human cells. Here, we made a direct comparison of DNA replication dynamics in two…
Jeroen van den Berg, Vincent van Batenburg, Alexander van Oudenaarden
In a human cell thousands of replication forks simultaneously coordinate the duplication of the entire genome. The rate at which this process occurs, might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed a technology…
Razie Yousefi, Maga Rowicka
The dynamics of DNA replication, activation of replication origins and elongation rate, depend on dNTP in ways that remain poorly understood. Here, we present RepliSim, a probabilistic computer model of DNA replication simulation, which is capable of simulating DNA replication not only in normal conditions, but also…
Dean Y. Huang, Anna E. Johnson, Brandon S. Sim, Teresa W. Lo + 2 more
'Houra Merrikh' 'Paul A. Wiggins'] An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell, where a crowded cytoplasm as well as competing and potentially antagonistic…
Karl-Uwe Reusswig, Julia Bittmann, Martina Peritore, Mathilde Courtes + 4 more
'Mathilde Courtes' 'Benjamin Pardo' 'Michael Wierer' 'Matthias Mann' 'Boris Pfander'] DNA replicates once per cell cycle. Interfering with the regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineer…
Michel G. Gauthier, Antoine Dubé, John Bechhoefer
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets obtained by molecular combing, a widely used experimental technique for probing…
Florian Pflug, Deepak Bhat, Simone Pigolotti
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and genome stability. Qualitatively, in a growing cell culture, one expects that…
Omer Markovitch, Juntian Wu, Otto Sijbren
Copying information is vital for life's propagation. Current life forms maintain a low error rate in replication using complex machinery to prevent and correct errors. However, primitive life had to deal with higher error rates, limiting its ability to evolve. Discovering mechanisms to reduce errors would alleviate…
Authors not listed
DNA polymerases are essential enzymes responsible for accurate genome replication and repair, with divalent metal cofactors playing a crucial role in their catalytic function. Polymerase gamma (Pol γ) is the primary DNA polymerase in mitochondria, ensuring the faithful replication of mitochondrial DNA. The choice of…