The dynamics of genome replication using deep sequencing

Müller, Carolin A. and Hawkins, Michelle and Retkute, Renata and Malla, Sunir and Wilson, Ray and Blythe, Martin J. and Nakato, Ryuichiro and Komata, Makiko and Shirahige, Katsuhiko and de Moura, Alessandro P.S. and Nieduszynski, Conrad A. (2014) The dynamics of genome replication using deep sequencing. Nucleic Acids Research, 42 (1). e3/1-e3/11. ISSN 0305-1048

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Abstract

Eukaryotic genomes are replicated from multiple DNA replication origins. We present complementary deep sequencing approaches to measure origin location and activity in Saccharomyces cerevisiae. Measuring the increase in DNA copy number during a synchronous S-phase allowed the precise determination of genome replication. To map origin locations, replication forks were stalled close to their initiation sites; therefore, copy number enrichment was limited to origins. Replication timing profiles were generated from asynchronous cultures using fluorescence-activated cell sorting. Applying this technique we show that the replication profiles of haploid and diploid cells are indistinguishable, indicating that both cell types use the same cohort of origins with the same activities. Finally, increasing sequencing depth allowed the direct measure of replication dynamics from an exponentially growing culture. This is the first time this approach, called marker frequency analysis, has been successfully applied to a eukaryote. These data provide a high-resolution resource and methodological framework for studying genome biology.

Item Type: Article
Schools/Departments: University of Nottingham UK Campus > Faculty of Medicine and Health Sciences > School of Life Sciences > School of Biology
Depositing User: Liu, Mr Zhenxing
Date Deposited: 15 Apr 2014 11:06
Last Modified: 16 Sep 2016 18:03
URI: http://eprints.nottingham.ac.uk/id/eprint/2524

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