Mapping DNA replication with nanopore sequencing

Hennion, M.; Arbona, J.-M.; Cruaud, C.; Proux, F.; Le Tallec, B.; Novikova, E.; Engelen, S.; Lemainque, A.; Audit, B.; Hyrien, O.

doi:10.1101/426858

bioRxiv · 10.1101/426858

Mapping DNA replication with nanopore sequencing

Hennion, M.·Arbona, J.-M.·Cruaud, C.·Proux, F.·Le Tallec, B.·Novikova, E.·Engelen, S.·Lemainque, A.·Audit, B.·Hyrien, O.

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Abstract

We have harnessed nanopore sequencing to study DNA replication genome-wide at the single-molecule level. Using in vitro prepared DNA substrates, we characterized the effect of bromodeoxyuridine (BrdU) substitution for thymidine on the MinION nanopore electrical signal. Using a neural-network basecaller trained on yeast DNA containing either BrdU or thymidine, we identified BrdU-labelled tracts in yeast cells synchronously entering S phase in the presence of hydroxyurea and BrdU. As expected, the BrdU-labelled tracts coincided with previously identified early-firing, but not late-firing, replication origins. These results open the way to high-throughput, high-resolution, single-molecule analysis of DNA replication in many experimental systems.

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Hennion, M., Arbona, J.-M., Cruaud, C., Proux, F., Le Tallec, B., Novikova, E., Engelen, S., Lemainque, A., Audit, B., Hyrien, O.. 2018-09-26. Mapping DNA replication with nanopore sequencing. https://doi.org/10.1101/426858

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