Organization of DNA Replication Origin Firing in Xenopus Egg Extracts: The Role of Intra-S Checkpoint

During cell division, the duplication of the genome starts at multiple positions called replication origins. Origin firing requires the interaction of rate-limiting factors with potential origins during the S(ynthesis)-phase of the cell cycle. Origins fire as synchronous clusters which is proposed to be regulated by the intra-S checkpoint. By modelling the unchallenged, the checkpoint-inhibited and the checkpoint protein Chk1 over-expressed replication pattern of single DNA molecules from Xenopus sperm chromatin replicated in egg extracts, we demonstrate that the quantitative modelling of data requires: 1) a segmentation of the genome into regions of low and high probability of origin firing; 2) that regions with high probability of origin firing escape intra-S checkpoint regulation and 3) the variability of the rate of DNA synthesis close to replication forks is a necessary ingredient that should be taken in to account in order to describe the dynamic of replication origin firing. This model implies that the observed origin clustering emerges from the apparent synchrony of origin firing in regions with high probability of origin firing and challenge the assumption that the intra-S checkpoint is the main regulator of origin clustering. Author summary DNA replication is one of the fundamental cell functions. The genome of eukaryotic organisms is duplicated from multiple positions named replication origins. Single molecule experiments allow to visualise the dynamics of spatio-temporal patterns created during replication process. The dynamic of replication process is regulated by checkpoints. However, the influence and the role of checkpoint regulation in the dynamics of spatio-temporal patterns of DNA replication is not understood. In this work we build a minimal, process-based and data rooted numerical model that allows to decipher the impact of checkpoint regulation on the dynamics of spatio-temporal pattern of DNA replication.

[1]  Kyle N. Klein,et al.  Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication , 2020, bioRxiv.

[2]  Peiyao A. Zhao,et al.  High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells , 2020, Genome Biology.

[3]  M. Skrzypczak,et al.  Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication. , 2020, Molecular cell.

[4]  N. Gilbert,et al.  Negative supercoil at gene boundaries modulates gene topology , 2020, Nature.

[5]  Maga Rowicka,et al.  Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication , 2019, PLoS Comput. Biol..

[6]  M. Altmeyer,et al.  Basal CHK1 activity safeguards its stability to maintain intrinsic S-phase checkpoint functions , 2019, The Journal of cell biology.

[7]  Simon C Watkins,et al.  An ATR and CHK1 kinase signaling mechanism that limits origin firing during unperturbed DNA replication , 2019, Proceedings of the National Academy of Sciences.

[8]  Diletta Ciardo,et al.  On the Interplay of the DNA Replication Program and the Intra-S Phase Checkpoint Pathway , 2019, Genes.

[9]  Alain Arneodo,et al.  The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation , 2018, eLife.

[10]  A. Genovesio,et al.  High-throughput optical mapping of replicating DNA , 2017, bioRxiv.

[11]  P. Knipscheer,et al.  Xenopus egg extract: A powerful tool to study genome maintenance mechanisms. , 2017, Developmental biology.

[12]  A. Koren,et al.  DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation , 2017, Genome research.

[13]  M. Vergassola,et al.  Waves of Cdk1 Activity in S Phase Synchronize the Cell Cycle in Drosophila Embryos. , 2016, Developmental cell.

[14]  O. Hyrien,et al.  Single-molecule, antibody-free fluorescent visualisation of replication tracts along barcoded DNA molecules. , 2016, The International journal of developmental biology.

[15]  Corella S. Casas-Delucchi,et al.  3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression , 2016, Nature Communications.

[16]  Y. D'Aubenton-Carafa,et al.  Replication landscape of the human genome , 2016, Nature Communications.

[17]  Françoise Argoul,et al.  Structural organization of human replication timing domains , 2015, FEBS letters.

[18]  Scott Cheng‐Hsin Yang,et al.  Replication timing is regulated by the number of MCMs loaded at origins , 2015, Genome research.

[19]  A. Goldar,et al.  Tight Chk1 Levels Control Replication Cluster Activation in Xenopus , 2015, PloS one.

[20]  S. Bell,et al.  Single-Molecule Studies of Origin Licensing Reveal Mechanisms Ensuring Bidirectional Helicase Loading , 2015, Cell.

[21]  A. Shevchenko,et al.  Interaction of Chk1 with Treslin negatively regulates the initiation of chromosomal DNA replication. , 2015, Molecular cell.

[22]  Sven Bilke,et al.  A chromatin structure‐based model accurately predicts DNA replication timing in human cells , 2014, Molecular systems biology.

[23]  N. Rhind,et al.  DNA replication timing. , 2013, Cold Spring Harbor perspectives in biology.

[24]  Alain Arneodo,et al.  Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm , 2012, Nature Protocols.

[25]  Benjamin Audit,et al.  Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines , 2012, PLoS Comput. Biol..

[26]  Ryuichiro Nakato,et al.  Origin Association of Sld3, Sld7, and Cdc45 Proteins Is a Key Step for Determination of Origin-Firing Timing , 2011, Current Biology.

[27]  Alain Arneodo,et al.  Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome , 2011, PLoS Comput. Biol..

[28]  A. Donaldson,et al.  Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast , 2011, The EMBO journal.

[29]  D. Jackson,et al.  How dormant origins promote complete genome replication. , 2011, Trends in biochemical sciences.

[30]  J. Blow,et al.  Chk1 inhibits replication factory activation but allows dormant origin firing in existing factories , 2010, The Journal of cell biology.

[31]  John Bechhoefer,et al.  Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing , 2010, Molecular systems biology.

[32]  J. Diffley,et al.  Checkpoint Dependent Inhibition of DNA Replication Initiation by Sld3 and Dbf4 Phosphorylation , 2010, Nature.

[33]  David Fenyö,et al.  GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome , 2010, Molecular systems biology.

[34]  J. Blow,et al.  Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels , 2010, The Journal of cell biology.

[35]  Olivier Hyrien,et al.  Universal Temporal Profile of Replication Origin Activation in Eukaryotes , 2009, PloS one.

[36]  Xin Quan Ge,et al.  A model for DNA replication showing how dormant origins safeguard against replication fork failure , 2009, EMBO reports.

[37]  John Bechhoefer,et al.  Control of DNA replication by anomalous reaction-diffusion kinetics. , 2009, Physical review letters.

[38]  David Collingwood,et al.  The Temporal Program of Chromosome Replication: Genomewide Replication in clb5Δ Saccharomyces cerevisiae , 2008, Genetics.

[39]  Dirk Schübeler,et al.  Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation , 2008, PLoS biology.

[40]  K. Marheineke,et al.  DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts , 2008, Nucleic acids research.

[41]  Olivier Hyrien,et al.  A Dynamic Stochastic Model for DNA Replication Initiation in Early Embryos , 2008, PloS one.

[42]  M. Méchali,et al.  Cdk1 and Cdk2 activity levels determine the efficiency of replication origin firing in Xenopus , 2008, The EMBO journal.

[43]  Vincenzo Costanzo,et al.  Plx1 is required for chromosomal DNA replication under stressful conditions , 2008, The EMBO journal.

[44]  Edison T. Liu,et al.  Global Profiling of DNA Replication Timing and Efficiency Reveals that Efficient Replication/Firing Occurs Late during S-Phase in S. pombe , 2007, PloS one.

[45]  John Herrick,et al.  Replication fork velocities at adjacent replication origins are coordinately modified during DNA replication in human cells. , 2007, Molecular biology of the cell.

[46]  D. Gillespie,et al.  Chk1 regulates the density of active replication origins during the vertebrate S phase , 2007, The EMBO journal.

[47]  Y. Pommier,et al.  The Intra-S-Phase Checkpoint Affects both DNA Replication Initiation and Elongation: Single-Cell and -DNA Fiber Analyses , 2007, Molecular and Cellular Biology.

[48]  L. Zou,et al.  Single- and double-stranded DNA: building a trigger of ATR-mediated DNA damage response. , 2007, Genes & development.

[49]  Jürg Bähler,et al.  Genome‐wide characterization of fission yeast DNA replication origins , 2006, The EMBO journal.

[50]  M. DePamphilis,et al.  Regulating the licensing of DNA replication origins in metazoa. , 2006, Current opinion in cell biology.

[51]  Anindya Dutta,et al.  Right Place, Right Time, and Only Once: Replication Initiation in Metazoans , 2005, Cell.

[52]  J. Bartek,et al.  Inhibition of Human Chk1 Causes Increased Initiation of DNA Replication, Phosphorylation of ATR Targets, and DNA Breakage , 2005, Molecular and Cellular Biology.

[53]  J. Bechhoefer,et al.  Nucleation and growth in one dimension. I. The generalized Kolmogorov-Johnson-Mehl-Avrami model. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[54]  J. Bechhoefer,et al.  Nucleation and growth in one dimension. II. Application to DNA replication kinetics. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[55]  K. Marheineke,et al.  Control of Replication Origin Density and Firing Time in Xenopus Egg Extracts , 2004, Journal of Biological Chemistry.

[56]  John Herrick,et al.  Persistence Length of Chromatin Determines Origin Spacing in Xenopus Early-Embryo DNA Replication: Quantitative Comparisons between Theory and Experiment , 2003, Cell cycle.

[57]  Olivier Hyrien,et al.  Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[58]  Yves Pommier,et al.  [Cell cycle and checkpoints in oncology: new therapeutic targets]. , 2003, Medecine sciences : M/S.

[59]  K. Cimprich,et al.  A requirement for replication in activation of the ATR-dependent DNA damage checkpoint. , 2002, Genes & development.

[60]  T. Prokhorova,et al.  MCM2–7 Complexes Bind Chromatin in a Distributed Pattern Surrounding the Origin Recognition Complex inXenopus Egg Extracts* , 2002, The Journal of Biological Chemistry.

[61]  M. Stokes,et al.  DNA replication is required for the checkpoint response to damaged DNA in Xenopus egg extracts , 2002, The Journal of cell biology.

[62]  John Herrick,et al.  Kinetic model of DNA replication in eukaryotic organisms. , 2001, Journal of molecular biology.

[63]  Ronald W. Davis,et al.  Replication dynamics of the yeast genome. , 2001, Science.

[64]  C. Smythe,et al.  Activation of mammalian Chk1 during DNA replication arrest , 2001, The Journal of cell biology.

[65]  O. Hyrien,et al.  Aphidicolin Triggers a Block to Replication Origin Firing inXenopus Egg Extracts* , 2001, The Journal of Biological Chemistry.

[66]  J. Blow,et al.  Replication Origins in XenopusEgg Extract Are 5–15 Kilobases Apart and Are Activated in Clusters That Fire at Different Times , 2001, The Journal of cell biology.

[67]  D. Gilbert,et al.  Temporally coordinated assembly and disassembly of replication factories in the absence of DNA synthesis , 2000, Nature Cell Biology.

[68]  A Bensimon,et al.  Replication fork density increases during DNA synthesis in X. laevis egg extracts. , 2000, Journal of molecular biology.

[69]  O. Hyrien,et al.  Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos. , 2000, Journal of molecular biology.

[70]  Ben-Naim,et al.  Nucleation and growth in one dimension. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[71]  M. Méchali,et al.  Transition in Specification of Embryonic Metazoan DNA Replication Origins , 1995, Science.

[72]  M. Méchali,et al.  Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. , 1993, The EMBO journal.

[73]  J. Blow,et al.  DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts. , 1992, Nucleic acids research.

[74]  M. Méchali,et al.  Plasmid replication in Xenopus eggs and egg extracts: a 2D gel electrophoretic analysis. , 1992, Nucleic acids research.

[75]  Lennart Ljung,et al.  System Identification: Theory for the User , 1987 .

[76]  M. Méchali,et al.  Lack of specific sequence requirement for DNA replication in Xenopus eggs compared with high sequence specificity in yeast , 1984, Cell.

[77]  R. Harland,et al.  Regulated replication of DNA microinjected into eggs of Xenopus laevis , 1980, Cell.

[78]  P. R. Bevington,et al.  Data Reduction and Error Analysis for the Physical Sciences , 1969 .