Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

Carolin A. Müller, Michael A. Boemo, Paolo Spingardi, Benedikt M. Kessler, Skirmantas Kriaucionis, Jared T. Simpson, Conrad A. Nieduszynski

Research output: Contribution to journalArticlepeer-review

40 Citations (Scopus)

Abstract

Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20–160 kilobases to generate a whole-genome single-molecule map of DNA replication dynamics and discover a class of low-frequency stochastic origins in budding yeast. The D-NAscent software is available at https://github.com/MBoemo/DNAscent.git.

Original languageEnglish
Pages (from-to)429-436
Number of pages8
JournalNature Methods
Volume16
Issue number5
Early online date22 Apr 2019
DOIs
Publication statusPublished - May 2019

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