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Michael Boemo - Untangling heterogeneity in DNA replication with nanopore sequencing

London Calling 2019

Genome replication is a stochastic process whereby each cell exhibits different patterns of origin activation and replication fork movement. Despite this heterogeneity, replication is a remarkably stable process that works quickly and correctly over hundreds of thousands of iterations. Existing methods for measuring replication dynamics largely focus on how a population of cells behave on average, which precludes the detection of low probability errors that may have occurred in individual cells. These errors can have a severe impact on genome integrity, yet existing single-molecule methods, such as DNA combing, are too costly, low-throughput, and low-resolution to effectively detect them. We have created a method called D-NAscent that uses Oxford Nanopore sequencing to create high-throughput genome-wide maps of DNA replication dynamics in single molecules. I will discuss the informatics approach that our software uses, as well as questions pertaining to DNA replication and genome stability that our method is uniquely positioned to answer.

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Michael Boemo from the University of Oxford began by introducing genome replication describing it as a stochastic process where each cell exhibits different patterns of origin activation and replication fork movement. Despite this unpredictable nature replication is actually a very stable process that works quickly and correctly over hundreds of thousands of iterations. Michael explained that current methods largely use a population of cells to study for measuring replication dynamics other and existing single-molecule methods, such as DNA combing, are low-throughput and expensive. He then introduced a method called D-NAscent using Nanopore sequencing to create high-throughput genome-wide maps of DNA replication dynamics in single molecules.

D-Nascent requires a brief pulse treatment of BrdU on replicating cells, during the BrdU treatment any DNA synthesis will incorporate BRdU instead of Thymine, marking the actively replicating regions. Combining this BrdU labelling with nanopore sequencing enables the identification of replicating regions because the Thymine analogue BrdU creates a different current disruption when passing through the nanopore to the canonical Thymine base. These replication origins are at single molecule level at high resolution.

Pilling up the reads and comparing origin sites to population level data (ensembl) the D-Nascent data matched very well. Looking at individual reads stretches of BrdU map well to known replication origins further validating the method. As well as enabling identification of  origin location this method can also be used to look at fork direction and velocity. Michael validated the directionality using the well studied origin at rDNA locus. The long nanopore reads also enable multiple origins firing to be identified in a single read enabling the study of synchronicity or origin firing.

The paper describing the method was recently published in Nature Methods: Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.

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