FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Abstract Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication...

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Main Authors: Magali Hennion, Jean-Michel Arbona, Laurent Lacroix, Corinne Cruaud, Bertrand Theulot, Benoît Le Tallec, Florence Proux, Xia Wu, Elizaveta Novikova, Stefan Engelen, Arnaud Lemainque, Benjamin Audit, Olivier Hyrien
Format: Article
Language:English
Published: BMC 2020-05-01
Series:Genome Biology
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Online Access:http://link.springer.com/article/10.1186/s13059-020-02013-3
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author Magali Hennion
Jean-Michel Arbona
Laurent Lacroix
Corinne Cruaud
Bertrand Theulot
Benoît Le Tallec
Florence Proux
Xia Wu
Elizaveta Novikova
Stefan Engelen
Arnaud Lemainque
Benjamin Audit
Olivier Hyrien
author_facet Magali Hennion
Jean-Michel Arbona
Laurent Lacroix
Corinne Cruaud
Bertrand Theulot
Benoît Le Tallec
Florence Proux
Xia Wu
Elizaveta Novikova
Stefan Engelen
Arnaud Lemainque
Benjamin Audit
Olivier Hyrien
author_sort Magali Hennion
collection DOAJ
description Abstract Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,651 replication tracks reproducing population-based replication directionality profiles and map 4964 and 4485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.
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spelling doaj.art-207b69b66bc4499fb532f23fff185faf2022-12-21T17:13:21ZengBMCGenome Biology1474-760X2020-05-0121112510.1186/s13059-020-02013-3FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencingMagali Hennion0Jean-Michel Arbona1Laurent Lacroix2Corinne Cruaud3Bertrand Theulot4Benoît Le Tallec5Florence Proux6Xia Wu7Elizaveta Novikova8Stefan Engelen9Arnaud Lemainque10Benjamin Audit11Olivier Hyrien12Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de PhysiqueInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLCommissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de biologie François-Jacob, GenoscopeInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLCommissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de biologie François-Jacob, GenoscopeCommissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de biologie François-Jacob, GenoscopeUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de PhysiqueInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSLAbstract Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,651 replication tracks reproducing population-based replication directionality profiles and map 4964 and 4485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.http://link.springer.com/article/10.1186/s13059-020-02013-3DNA replicationNanopore sequencingBromodeoxyuridineSingle-molecule analysisS. cerevisiaeConvolutional neural network
spellingShingle Magali Hennion
Jean-Michel Arbona
Laurent Lacroix
Corinne Cruaud
Bertrand Theulot
Benoît Le Tallec
Florence Proux
Xia Wu
Elizaveta Novikova
Stefan Engelen
Arnaud Lemainque
Benjamin Audit
Olivier Hyrien
FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
Genome Biology
DNA replication
Nanopore sequencing
Bromodeoxyuridine
Single-molecule analysis
S. cerevisiae
Convolutional neural network
title FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
title_full FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
title_fullStr FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
title_full_unstemmed FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
title_short FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
title_sort fork seq replication landscape of the saccharomyces cerevisiae genome by nanopore sequencing
topic DNA replication
Nanopore sequencing
Bromodeoxyuridine
Single-molecule analysis
S. cerevisiae
Convolutional neural network
url http://link.springer.com/article/10.1186/s13059-020-02013-3
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