Read all about it!

Our papers (group members’ names in bold; find papers at PubMed or Google scholar; read our pre-prints on biorxiv):

  • Prusokas, A, Hawkins, M, Nieduszynski, CA, Retkute, R. Effectiveness of glass beads for plating cell cultures. Phys Rev E. 2021;103 (5-1):052410. doi: 10.1103/PhysRevE.103.052410. PubMed PMID:34134194 .
  • Cooke, SL, Soares, BL, Müller, CA, Nieduszynski, CA, Bastos de Oliveira, FM, de Bruin, RAM. Tos4 mediates gene expression homeostasis through interaction with HDAC complexes independently of H3K56 acetylation. J Biol Chem. ;296 :100533. doi: 10.1016/j.jbc.2021.100533. PubMed PMID:33713703 PubMed Central PMC8054192.
  • Hoggard, T, Müller, CA, Nieduszynski, CA, Weinreich, M, Fox, CA. Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early- and late-replicating euchromatin. Proc Natl Acad Sci U S A. 2020;117 (25):14314-14321. doi: 10.1073/pnas.2004664117. PubMed PMID:32513739 PubMed Central PMC7322022.
  • 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 (3):e1007651. doi: 10.1371/journal.pcbi.1007651. PubMed PMID:32150540 PubMed Central PMC7082070.

  • Batrakou, DG, Müller, CA, Wilson, RHC, Nieduszynski, CA. DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family. Nat Protoc. 2020;15 (3):1255-1284. doi: 10.1038/s41596-019-0287-7. PubMed PMID:32051615 .
A step-by-step protocol to measure genome replication dynamics by high-throughput sequencing.

During S phase, the relative DNA copy number increases for each region as it is replicated; therefore, measuring DNA copy number can be used as a proxy for replication time. Here we present a step-by-step protocol to determine genome replication dynamics using high-throughput DNA sequencing to measure DNA copy-number. Cell populations can be obtained in three variants of the method: sort-seq, sync-seq and MFA-seq.

We have shared our computational pipeline and example sequence data.

  • Donaldson, AD, Nieduszynski, CA. Genome-wide analysis of DNA replication timing in single cells: Yes! We're all individuals. Genome Biol. 2019;20 (1):111. doi: 10.1186/s13059-019-1719-y. PubMed PMID:31146781 PubMed Central PMC6541995.
  • Tong, P, Pidoux, AL, Toda, NRT, Ard, R, Berger, H, Shukla, M, Torres-Garcia, J, Müller, CA, Nieduszynski, CA, Allshire, RC. Interspecies conservation of organisation and function between nonhomologous regional centromeres. Nat Commun. 2019;10 (1):2343. doi: 10.1038/s41467-019-09824-4. PubMed PMID:31138803 PubMed Central PMC6538654.

  • Müller, CA, Boemo, MA, Spingardi, P, Kessler, BM, Kriaucionis, S, Simpson, JT, Nieduszynski, CA. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nat Methods. 2019;16 (5):429-436. doi: 10.1038/s41592-019-0394-y. PubMed PMID:31011185 .
D-NAscent: nanopore DNA sequencing can distinguish thymidine from analogues to allow single-molecule analysis of genome replication.

DNA replication initiation is stochastic and obscured in population datasets. In this paper we introduce D-NAscent: a method to detect base analogs in ultra-long nanopore sequencing reads. This allowed us to identify replication origins and replication fork movement genome-wide on sequence reads of 20–160 kilobases. Our study marks the first, whole genome characterisation of DNA replication dynamics on single-molecules.

We have shared both the D-NAscent software and underlying sequence data.

Featured as a Research Highlight by our department.

  • Bazarova, A, Nieduszynski, CA, Akerman, I, Burroughs, NJ. Bayesian inference of origin firing time distributions, origin interference and licencing probabilities from Next Generation Sequencing data. Nucleic Acids Res. 2019;47 (5):2229-2243. doi: 10.1093/nar/gkz094. PubMed PMID:30859196 PubMed Central PMC6412128.

Loss of cohesin does not disrupt replication timing.

In this study we address the long-standing question: Do topologically associating domains (TADs) act as a causative organizing structure for replication timing domains? Using rapid and complete cohesin degradation we observe no perturbations to replication timing. Our results suggest that cohesin-mediated genome architecture is not required for replication timing patterns.

  • Batrakou, DG, Heron, ED, Nieduszynski, CA. Rapid high-resolution measurement of DNA replication timing by droplet digital PCR. Nucleic Acids Res. 2018;46 (19):e112. doi: 10.1093/nar/gky590. PubMed PMID:29986073 PubMed Central PMC6212846.
Droplet digital PCR measurement of DNA replication time.

In this paper we describe the use of digital PCR to precisely and rapidly measure DNA copy number as a proxy for replication time. As a proof-of-principle we demonstrate the method’s utility for the study of DNA replication time in both yeast and human cells. We show the power of the method by undertaking a targeted screen of kinetochore mutants to discover those that affect centromere replication time.

As part of this work we generated whole genome DNA replication timing data (sort-seq) for cultured human cells (HeLa). These data can be visualised via the link to our UCSC genome browser hub on the resources page.

Featured as a Research Highlight by our department.

  • Wallis, ABA, Nieduszynski, CA. Investigating the role of Rts1 in DNA replication initiation. Wellcome Open Res. 2018;3 :23. doi: 10.12688/wellcomeopenres.13884.1. PubMed PMID:29721551 PubMed Central PMC5897792.
  • Ausiannikava, D, Mitchell, L, Marriott, H, Smith, V, Hawkins, M, Makarova, KS, Koonin, EV, Nieduszynski, CA, Allers, T. Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii. Mol Biol Evol. 2018;35 (8):1855-1868. doi: 10.1093/molbev/msy075. PubMed PMID:29668953 PubMed Central PMC6063281.
  • Kedziora, S, Gali, VK, Wilson, RHC, Clark, KRM, Nieduszynski, CA, Hiraga, SI, Donaldson, AD. Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast. Nucleic Acids Res. 2018;46 (8):3993-4003. doi: 10.1093/nar/gky132. PubMed PMID:29529242 PubMed Central PMC5934629.

DNA replication timing influences the expression level of some genes.

Chromosomes replicate in a characteristic and reproducible temporal order. However, it has been unknown whether there is a physiological requirement for the regulation of replication timing. In this paper, we report our discovery that early DNA replication is required for the highest expression levels of certain genes.

Highlighted in J. Cell Biol. by María Gómez, selected for the Nuclear biology special collection by Ana Pombo and selected for the DNA replication and genome instability special collection by Agata Smogorzewska.

Selected as “of outstanding interest” by Mirit Aladjem and colleagues in their Current Opinion in Cell Biology review.

  • Shen, Y, Wang, Y, Chen, T, Gao, F, Gong, J, Abramczyk, D, Walker, R, Zhao, H, Chen, S, Liu, W, Luo, Y, Müller, CA, Paul-Dubois-Taine, A, Alver, B, Stracquadanio, G, Mitchell, LA, Luo, Z, Fan, Y, Zhou, B, Wen, B, Tan, F, Wang, Y, Zi, J, Xie, Z, Li, B, Yang, K, Richardson, SM, Jiang, H, French, CE, Nieduszynski, CA, Koszul, R, Marston, AL, Yuan, Y, Wang, J, Bader, JS, Dai, J, Boeke, JD, Xu, X, Cai, Y, Yang, H. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science. 2017;355 (6329):. doi: 10.1126/science.aaf4791. PubMed PMID:28280153 PubMed Central PMC5390853.
  • Kobayashi, N, Suzuki, Y, Schoenfeld, LW, Müller, CA, Nieduszynski, C, Wolfe, KH, Tanaka, TU. Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres. Curr Biol. 2015;25 (15):2026-33. doi: 10.1016/j.cub.2015.06.023. PubMed PMID:26166782 PubMed Central PMC4533239.
  • Daigaku, Y, Keszthelyi, A, Müller, CA, Miyabe, I, Brooks, T, Retkute, R, Hubank, M, Nieduszynski, CA, Carr, AM. A global profile of replicative polymerase usage. Nat Struct Mol Biol. 2015;22 (3):192-198. doi: 10.1038/nsmb.2962. PubMed PMID:25664722 PubMed Central PMC4789492.
Polymerases at the replication fork.

This collaborative study reveals that polymerase epsilon is responsible for leading strand synthesis, with polymerase delta undertaking lagging strand synthesis. Our polymerase usage data directly maps replication origin location, quantifies origin efficiency, reveals that replication termination events are dispersed across large termination zones and indirectly estimates replication timing.

With associated News & Views by Sue Jinks-Robertson & Hannah L Klein.

  • Hawkins, M, Retkute, R, Müller, CA, Saner, N, Tanaka, TU, de Moura, AP, Nieduszynski, CA. High-resolution replication profiles define the stochastic nature of genome replication initiation and termination. Cell Rep. 2013;5 (4):1132-41. doi: 10.1016/j.celrep.2013.10.014. PubMed PMID:24210825 PubMed Central PMC3898788.
Stochastic mathematical models aid in the interpretation of whole genome replication timing data.

In this study we used a combination of high-resolution, genomic-wide DNA replication data, mathematical modelling and single cell experiments to reveal the stochastic nature of replication initiation and termination. We find that the homogeneous picture implied by ensemble datasets masks biologically significant cell-to-cell variation in genome replication.

  • Hawkins, M, Malla, S, Blythe, MJ, Nieduszynski, CA, Allers, T. Accelerated growth in the absence of DNA replication origins. Nature. 2013;503 (7477):544-547. doi: 10.1038/nature12650. PubMed PMID:24185008 PubMed Central PMC3843117.
Relative DNA copy number reveals replication origin sites as peaks.

We discovered that the halophilic archaea, Haloferax volcanii, not only can survive in the absence of DNA replication origins, but also has accelerated growth.

This work is recommended in F1000 and featured in a research highlight in Nature Reviews Microbiology.

See associated article at The Conversation.

  • Müller, CA, Hawkins, M, Retkute, R, Malla, S, Wilson, R, Blythe, MJ, Nakato, R, Komata, M, Shirahige, K, de Moura, AP, Nieduszynski, CA. The dynamics of genome replication using deep sequencing. Nucleic Acids Res. 2014;42 (1):e3. doi: 10.1093/nar/gkt878. PubMed PMID:24089142 PubMed Central PMC3874191.
High-throughput sequencing reveals the dynamics of genome replication.

This paper describes and rigorously validates a range of next generation sequencing approaches to reveal at unprecedented resolution the temporal order of genome replication. My research group and others are applying these sequencing approaches to a range of questions in a variety of organisms.

  • Hoggard, T, Shor, E, Müller, CA, Nieduszynski, CA, Fox, CA. A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast. PLoS Genet. 2013;9 (9):e1003798. doi: 10.1371/journal.pgen.1003798. PubMed PMID:24068963 PubMed Central PMC3772097.
  • Saner, N, Karschau, J, Natsume, T, Gierlinski, M, Retkute, R, Hawkins, M, Nieduszynski, CA, Blow, JJ, de Moura, AP, Tanaka, TU. Stochastic association of neighboring replicons creates replication factories in budding yeast. J Cell Biol. 2013;202 (7):1001-12. doi: 10.1083/jcb.201306143. PubMed PMID:24062338 PubMed Central PMC3787376.
  • Newman, TJ, Mamun, MA, Nieduszynski, CA, Blow, JJ. Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts. Nucleic Acids Res. 2013;41 (21):9705-18. doi: 10.1093/nar/gkt728. PubMed PMID:23963700 PubMed Central PMC3834809.
  • Rudolph, CJ, Upton, AL, Stockum, A, Nieduszynski, CA, Lloyd, RG. Avoiding chromosome pathology when replication forks collide. Nature. 2013;500 (7464):608-11. doi: 10.1038/nature12312. PubMed PMID:23892781 PubMed Central PMC3819906.
  • Natsume, T, Müller, CA, Katou, Y, Retkute, R, Gierliński, M, Araki, H, Blow, JJ, Shirahige, K, Nieduszynski, CA, Tanaka, TU. Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment. Mol Cell. 2013;50 (5):661-74. doi: 10.1016/j.molcel.2013.05.011. PubMed PMID:23746350 PubMed Central PMC3679449.
Recruitment of Dbf4-Cdc7 to the kinetochore promotes activation of proximal origins early in S phase.

We discovered that kinetochore recruitment of the Dbf4-dependent kinase ensures early centromere replication. Mutations that delay centromere replication give rise to elevated chromosome loss, revealing the first physiological role for temporal regulation of genome replication.

This work is recommended in F1000.

  • Liti, G, Nguyen Ba, AN, Blythe, M, Müller, CA, Bergström, A, Cubillos, FA, Dafhnis-Calas, F, Khoshraftar, S, Malla, S, Mehta, N, Siow, CC, Warringer, J, Moses, AM, Louis, EJ, Nieduszynski, CA. High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genomics. 2013;14 :69. doi: 10.1186/1471-2164-14-69. PubMed PMID:23368932 PubMed Central PMC3599269.
  • Retkute, R, Nieduszynski, CA, de Moura, A. Mathematical modeling of genome replication. Phys Rev E Stat Nonlin Soft Matter Phys. 2012;86 (3 Pt 1):031916. doi: 10.1103/PhysRevE.86.031916. PubMed PMID:23030953 PubMed Central PMC3671344.
  • Müller, CA, Nieduszynski, CA. Conservation of replication timing reveals global and local regulation of replication origin activity. Genome Res. 2012;22 (10):1953-62. doi: 10.1101/gr.139477.112. PubMed PMID:22767388 PubMed Central PMC3460190.
A few replication origins differ in activity between closely related species, revealing that local sequence elements control origin activity.

We found that the temporal order of genome replication is conserved between species. The discovery of a minority of DNA replication origins that have evolved different activities allowed us to demonstrate that origin activity is locally (cis) regulated.

  • Guttery, DS, Ferguson, DJ, Poulin, B, Xu, Z, Straschil, U, Klop, O, Solyakov, L, Sandrini, SM, Brady, D, Nieduszynski, CA, Janse, CJ, Holder, AA, Tobin, AB, Tewari, R. A putative homologue of CDC20/CDH1 in the malaria parasite is essential for male gamete development. PLoS Pathog. 2012;8 (2):e1002554. doi: 10.1371/journal.ppat.1002554. PubMed PMID:22383885 PubMed Central PMC3285604.
  • Siow, CC, Nieduszynska, SR, Müller, CA, Nieduszynski, CA. OriDB, the DNA replication origin database updated and extended. Nucleic Acids Res. 2012;40 (Database issue):D682-6. doi: 10.1093/nar/gkr1091. PubMed PMID:22121216 PubMed Central PMC3245157.
  • Retkute, R, Nieduszynski, CA, de Moura, A. Dynamics of DNA replication in yeast. Phys Rev Lett. 2011;107 (6):068103. doi: 10.1103/PhysRevLett.107.068103. PubMed PMID:21902372 PubMed Central PMC3671325.
  • Rhind, N, Chen, Z, Yassour, M, Thompson, DA, Haas, BJ, Habib, N, Wapinski, I, Roy, S, Lin, MF, Heiman, DI, Young, SK, Furuya, K, Guo, Y, Pidoux, A, Chen, HM, Robbertse, B, Goldberg, JM, Aoki, K, Bayne, EH, Berlin, AM, Desjardins, CA, Dobbs, E, Dukaj, L, Fan, L, FitzGerald, MG, French, C, Gujja, S, Hansen, K, Keifenheim, D, Levin, JZ, Mosher, RA, Müller, CA, Pfiffner, J, Priest, M, Russ, C, Smialowska, A, Swoboda, P, Sykes, SM, Vaughn, M, Vengrova, S, Yoder, R, Zeng, Q, Allshire, R, Baulcombe, D, Birren, BW, Brown, W, Ekwall, K, Kellis, M, Leatherwood, J, Levin, H, Margalit, H, Martienssen, R, Nieduszynski, CA, Spatafora, JW, Friedman, N, Dalgaard, JZ, Baumann, P, Niki, H, Regev, A, Nusbaum, C. Comparative functional genomics of the fission yeasts. Science. 2011;332 (6032):930-6. doi: 10.1126/science.1203357. PubMed PMID:21511999 PubMed Central PMC3131103.
  • Nieduszynski, CA, Liti, G. From sequence to function: Insights from natural variation in budding yeasts. Biochim Biophys Acta. 2011;1810 (10):959-66. doi: 10.1016/j.bbagen.2011.02.004. PubMed PMID:21320572 PubMed Central PMC3271348.
  • de Moura, AP, Retkute, R, Hawkins, M, Nieduszynski, CA. Mathematical modelling of whole chromosome replication. Nucleic Acids Res. 2010;38 (17):5623-33. doi: 10.1093/nar/gkq343. PubMed PMID:20457753 PubMed Central PMC2943597.

We present a mathematical model for whole chromosome replication, conceptualising how key molecular properties of DNA replication are related and demonstrating the wealth of information available in quantitative genomic datasets.

This work is recommended in F1000.

  • Shor, E, Warren, CL, Tietjen, J, Hou, Z, Müller, U, Alborelli, I, Gohard, FH, Yemm, AI, Borisov, L, Broach, JR, Weinreich, M, Nieduszynski, CA, Ansari, AZ, Fox, CA. The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication. PLoS Genet. 2009;5 (12):e1000755. doi: 10.1371/journal.pgen.1000755. PubMed PMID:19997491 PubMed Central PMC2778871.
  • Nieduszynski, CA, Donaldson, AD. Detection of replication origins using comparative genomics and recombinational ARS assay. Methods Mol Biol. 2009;521 :295-313. doi: 10.1007/978-1-60327-815-7_16. PubMed PMID:19563113 .
  • Chang, F, Theis, JF, Miller, J, Nieduszynski, CA, Newlon, CS, Weinreich, M. Analysis of chromosome III replicators reveals an unusual structure for the ARS318 silencer origin and a conserved WTW sequence within the origin recognition complex binding site. Mol Cell Biol. 2008;28 (16):5071-81. doi: 10.1128/MCB.00206-08. PubMed PMID:18573888 PubMed Central PMC2519699.
  • Nieduszynski, CA, Hiraga, S, Ak, P, Benham, CJ, Donaldson, AD. OriDB: a DNA replication origin database. Nucleic Acids Res. 2007;35 (Database issue):D40-6. doi: 10.1093/nar/gkl758. PubMed PMID:17065467 PubMed Central PMC1781122.
OriDB: a DNA replication origin database for budding and fission yeasts.

This paper presents the DNA replication origin database, OriDB, a catalogue of confirmed and predicted DNA replication origin sites. This database is an example of our commitment not only to sharing data, but also to making it highly accessible to the research community – see links on the resources page.

  • Nieduszynski, CA, Knox, Y, Donaldson, AD. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 2006;20 (14):1874-9. doi: 10.1101/gad.385306. PubMed PMID:16847347 PubMed Central PMC1522085.
Sequence conservation at replication origins reveals the location of the ORC-binding site.

This was the first paper to use comparative genomics to investigate DNA replication. We discovered that the functional sequence elements at DNA replication origins are evolutionarily conserved, leaving a phylogenetic footprint that allowed them to be pin- pointed genome-wide.

This work is recommended in F1000.

  • Nieduszynski, CA, Blow, JJ, Donaldson, AD. The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription. Nucleic Acids Res. 2005;33 (8):2410-20. doi: 10.1093/nar/gki539. PubMed PMID:15860777 PubMed Central PMC1087785.
  • Müller-Tidow, C, Ji, P, Diederichs, S, Potratz, J, Bäumer, N, Köhler, G, Cauvet, T, Choudary, C, van der Meer, T, Chan, WY, Nieduszynski, C, Colledge, WH, Carrington, M, Koeffler, HP, Restle, A, Wiesmüller, L, Sobczak-Thépot, J, Berdel, WE, Serve, H. The cyclin A1-CDK2 complex regulates DNA double-strand break repair. Mol Cell Biol. 2004;24 (20):8917-28. doi: 10.1128/MCB.24.20.8917-8928.2004. PubMed PMID:15456866 PubMed Central PMC517883.
  • van der Meer, T, Chan, WY, Palazon, LS, Nieduszynski, C, Murphy, M, Sobczak-Thépot, J, Carrington, M, Colledge, WH. Cyclin A1 protein shows haplo-insufficiency for normal fertility in male mice. Reproduction. 2004;127 (4):503-11. doi: 10.1530/rep.1.00131. PubMed PMID:15047941 .
  • Nieduszynski, CA, Murray, J, Carrington, M. Whole-genome analysis of animal A- and B-type cyclins. Genome Biol. 2002;3 (12):RESEARCH0070. doi: 10.1186/gb-2002-3-12-research0070. PubMed PMID:12537559 PubMed Central PMC151172.
  • Cosgrove, AJ, Nieduszynski, CA, Donaldson, AD. Ku complex controls the replication time of DNA in telomere regions. Genes Dev. 2002;16 (19):2485-90. doi: 10.1101/gad.231602. PubMed PMID:12368259 PubMed Central PMC187453.
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