FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing.
Bromodeoxyuridine
Convolutional neural network
DNA replication
Nanopore sequencing
Replication origins
S. cerevisiae
Single-molecule analysis
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
26 05 2020
26 05 2020
Historique:
received:
31
07
2019
accepted:
10
04
2020
entrez:
28
5
2020
pubmed:
28
5
2020
medline:
2
4
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32456659
doi: 10.1186/s13059-020-02013-3
pii: 10.1186/s13059-020-02013-3
pmc: PMC7251829
doi:
Substances chimiques
Bromodeoxyuridine
G34N38R2N1
Types de publication
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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