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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BMC
2020-05-01
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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. |
first_indexed | 2024-12-24T05:24:58Z |
format | Article |
id | doaj.art-207b69b66bc4499fb532f23fff185faf |
institution | Directory Open Access Journal |
issn | 1474-760X |
language | English |
last_indexed | 2024-12-24T05:24:58Z |
publishDate | 2020-05-01 |
publisher | BMC |
record_format | Article |
series | Genome Biology |
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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