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- 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.
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.
Featured as a Research Highlight by our department.
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.
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.
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
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.
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.
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.
We discovered that the halophilic archaea, Haloferax volcanii, not only can survive in the absence of DNA replication origins, but also has accelerated growth.
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.
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.
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.
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.
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.
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.
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.