ArticleNature protocols2020
Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 30 citations in OpenAlex.
- Single-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes.Nature communications · 2026Article
- Nuclear compartmentalization at the G1/S transition plays a key role in DNA replication control.Nature communications · 2026Article
- Spatial organization and dynamics of genome replication: from forks to foci.Nucleic acids research · 2026Review
- Parallel analysis of replication timing, gene expression, and copy number with PARTAGE.Genome research · 2026Article
- scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase.Nature communications · 2025Article
- ResNet-Powered Multi-Class Identification of Sequence Patterns for Genome Replication Timing Analysis.Interdisciplinary sciences, computational life sciences · 2025Article
- The long-standing relationship between replication timing, gene expression, and chromatin accessibility is maintained in early mouse embryogenesis.bioRxiv : the preprint server for biology · 2025Article
- PARTAGE: Parallel analysis of replication timing and gene expression.bioRxiv : the preprint server for biology · 2025Article
- Review
- Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER.Nature genetics · 2025Article
- Article
- Sex-specific DNA-replication in the early mammalian embryo.Nature communications · 2024Article
- DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility.Nature communications · 2024Article
- DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility.bioRxiv : the preprint server for biology · 2023Article
- Repli-seq Sample Preparation using Cell Sorting with Cell-Permeant Dyes.Current protocols · 2023Article
- Replication dynamics identifies the folding principles of the inactive X chromosome.Nature structural & molecular biology · 2023Article
- Origins of DNA replication in eukaryotes.Molecular cell · 2023Review
- The location and development of Replicon Cluster Domains in early replicating DNA.Wellcome open research · 2023Article
- Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
- Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression.The Journal of cell biology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require many S-phase cells for either the effective enrichment of replicating DNA through bromodeoxyuridine (BrdU) immunoprecipitation or the determination of copy-number differences during S-phase, which precludes their application to non-abundant cell types and single cells. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy-number differences that arise between replicated and unreplicated DNA. Haplotype-resolved scRepli-seq, which distinguishes pairs of homologous chromosomes within a single cell, is feasible by using single-nucleotide polymorphism (SNP)/indel information. We also provide computational pipelines for quality control, normalization, and binarization of the scRepli-seq data. The experimental portion of this protocol (before sequencing) takes 3 d.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.