Mapping DNA replication with nanopore sequencing

Hennion, Magali; Arbona, Jean-Michel; Cruaud, Corinne; Proux, Florence; Tallec, Benoît Le; Novikova, Elizaveta; Engelen, Stéfan; Lemainque, Arnaud; Audit, Benjamin; Hyrien, Olivier

doi:10.1101/426858

Cited by 13 publications

(19 citation statements)

References 34 publications

(42 reference statements)

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“…These shifts can be identified post-basecalling and post-alignment with three distinct methods: (a) without prior knowledge about the modification (de novo) by comparing to an in silico reference [105], or a control, non-modified sample (typically amplified DNA) [105,106]; (b) using a pre-trained model [66,107,108] (Fig. 3, Table 1); and (c) directly by a basecaller using an extended alphabet [45,109].…”

Section: Detecting Base Modificationsmentioning

confidence: 99%

“…A development basecaller, Taiyaki [45], can be trained for specific organisms or base modifications. RepNano can basecall BrdU in addition to the four canonical DNA bases [109]. Two major bottlenecks in the creation of modification-ready basecallers are the need for appropriate training data and the combinatorial complexity of adding bases to the basecalling alphabet.…”

Section: Detecting Base Modificationsmentioning

confidence: 99%

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Opportunities and challenges in long-read sequencing data analysis

et al. 2020

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Long-read sequencing technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of long-read sequencing projects, we review the current landscape of available tools and present an online interactive database, long-read-tools.org, to facilitate their browsing. We further focus on the principles of error correction, base modification detection, and long-read transcriptomics analysis and highlight the challenges that remain.

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Section: Detecting Base Modificationsmentioning

confidence: 99%

Section: Detecting Base Modificationsmentioning

confidence: 99%

Opportunities and challenges in long-read sequencing data analysis

et al. 2020

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“…Importantly, the nanopore sequencer can detect base modifications on long RNA and DNA molecules [7,8]; for review [9]. In particular, we and others reported the detection of bromodeoxyuridine (BrdU) or other thymidine analogs incorporated during DNA replication in yeast or mouse DNA [10,11,12]. Using S. cerevisiae cells synchronously progressing through S phase in conditions of limiting BrdU concentrations, Müller et al [11] detected gradients of BrdU incorporation along single DNA molecules at 2 kb resolution.…”

mentioning

confidence: 98%

FORK-seq: replication landscape of theSaccharomyces cerevisiaegenome by nanopore sequencing

Hennion

Arbona

Lacroix

et al. 2020

Preprint

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Genome replication mapping methods profile cell populations, masking cell-tocell 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 populationbased replication directionality profiles and map 4,964 and 4,485 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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“…For genome-wide analysis of DNA replication, pulse labeling of replication sites by base analogs, such as BrdU (bromodeoxyuridine), is widely used [71]. Attempts to detect base analogs directly using a Nanopore sequencer have been reported by some groups [72][73][74] (Fig. 3b).…”

Section: Detection Of Dna Replication Using Base Analogsmentioning

confidence: 99%

“…They also developed a BrU detection tool based on the HMM for D-Nascent. Hennion et al used BrU for the detection of DNA replication in S. cerevisiae [73]. They developed RepNano, which is a deep learning-based software, for BrU detection.…”

Section: Detection Of Dna Replication Using Base Analogsmentioning

confidence: 99%

Recent advances in the detection of base modifications using the Nanopore sequencer

Seki

2019

J Hum Genet

112

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DNA and RNA modifications have important functions, including the regulation of gene expression. Existing methods based on short-read sequencing for the detection of modifications show difficulty in determining the modification patterns of single chromosomes or an entire transcript sequence. Furthermore, the kinds of modifications for which detection methods are available are very limited. The Nanopore sequencer is a single-molecule, long-read sequencer that can directly sequence RNA as well as DNA. Moreover, the Nanopore sequencer detects modifications on long DNA and RNA molecules. In this review, we mainly focus on base modification detection in the DNA and RNA of mammals using the Nanopore sequencer. We summarize current studies of modifications using the Nanopore sequencer, detection tools using statistical tests or machine learning, and applications of this technology, such as analyses of open chromatin, DNA replication, and RNA metabolism.

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Mapping DNA replication with nanopore sequencing

Cited by 13 publications

References 34 publications

Opportunities and challenges in long-read sequencing data analysis

Opportunities and challenges in long-read sequencing data analysis

FORK-seq: replication landscape of theSaccharomyces cerevisiaegenome by nanopore sequencing

Recent advances in the detection of base modifications using the Nanopore sequencer

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