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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

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scRepli-Seq: A Powerful Tool to Study Replication Timing and Genome Instability.

Megumi Sakamoto¹, Sakino Hori¹, Asahi Yamamoto¹

¹Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan.

Cytogenetic and Genome Research

|December 1, 2022

Summary

Single-cell DNA replication sequencing (scRepli-seq) reveals novel chromosomal units called replication timing (RT) domains. This method also predicts 3D genome organization and aids in studying genome instability.

Keywords:

Chromosome instability Copy number analysis Mammalian chromosome Replication timing domain scRepli-seq

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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Omics technologies enable single-cell level studies of cellular processes.
Replication timing (RT) is a key epigenetic mark reflecting genome organization.

Purpose of the Study:

To introduce single-cell DNA replication sequencing (scRepli-seq) for measuring RT in single mammalian cells.
To characterize novel RT domains and their relationship with 3D genome structure.
To explore the utility of scRepli-seq in assessing genome instability.

Main Methods:

Development and application of scRepli-seq.
Analysis of copy number differences in replicating single cells.
Correlation of RT domains with Hi-C based A/B compartments.

Main Results:

Identification of previously unrecognized static and dynamic RT domains (hundreds of kilobases to megabases).
High correlation between RT domains and A/B compartments, enabling prediction of 3D genome organization.
Demonstration of scRepli-seq's applicability to genome instability studies.

Conclusions:

scRepli-seq is a powerful tool for dissecting genome organization and dynamics at the single-cell level.
RT domains provide insights into higher-order chromatin structure.
scRepli-seq has broad applications in epigenetics and genome stability research.