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Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing

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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Fig. 1: A stepwise overview of the scRepli-seq analysis of mid-S-phase cells.
Fig. 2: scRepli-seq analysis throughout S-phase.
Fig. 3: scRepli-seq of samples with a limited number of cells.
Fig. 4: Electropherogram of MultiNA DNA-1000 from the scRepli-seq experiment.
Fig. 5: A schematic overview of the data analysis.
Fig. 6: Examples of RT profiles obtained through Steps 92–97.
Fig. 7: X chromosome scRepli-seq profiles of a single female mESC and a day 7–differentiated cell.
Fig. 8: Directory structure.
Fig. 9: Distribution of the tag densities of single G1 and single mid-S-phase cells.
Fig. 10: Selection of control G1 cells.

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Data availability

The datasets used to generate the figures are deposited in the NCBI Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE138634, GSE108556, and GSE113985.

Code availability

The code used to analyze the scRepli-seq data in this study is available in Supplementary Software 14 and at https://github.com/kuzobuta/scRepliseq-Pipeline.

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Acknowledgements

We thank the Center for Molecular Biology and Genetics of Mie University for NGS services. We also thank S. Kuraku and members of his laboratory for assistance with NGS, F. Matsuzaki for the use of the FACS instrument, A. Tanigawa and Y. Kondo for technical assistance, S-i. Hiraga for technical assistance in the Docker analysis and helpful comments, and L. Choubani for helpful comments. This work was supported by a RIKEN CDB/BDR intramural grant to I.H.; an award from the Special Postdoctoral Researcher (SPDR) Program of RIKEN to S.T.; an award from the RIKEN ‘Epigenome Manipulation Project’ of the All-RIKEN Projects to I.H.; MEXT KAKENHI grants JP16H01405 (to S.-i.T.), JP18H05530 (to I.H.), and JP15H01462 and JP17H06426 (to K.N.); and JSPS KAKENHI grants JP19K06610 (to S.-i.T.), JP18K14681 (to S.T.), and JP15K06942 (to K.N.).

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Contributions

H.M., S.T., T.S., I.H., and S.-i.T. conceived the project. S.T., T.S., and S.-i.T. developed and conducted scRepli-seq. H.M. established the scRepli-seq data analysis pipeline. S.T., T.S., I.H. and S.-i.T. performed cell culture and sample collection. K.N. and C.O. constructed a diploid reference genome and helped with the haplotype-resolved analysis pipeline setup. K.O. and M.O. supported the design and execution of the project. H.M., S.T., I.H. and S.-i.T. wrote the manuscript.

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Correspondence to Ichiro Hiratani or Shin-ichiro Takebayashi.

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Takahashi, S. et al. Nat. Genet. 51, 529–540 (2019): https://doi.org/10.1038/s41588-019-0347-5

Miura, H. et al. Nat. Genet. 51, 1356–1368 (2019): https://doi.org/10.1038/s41588-019-0474-z

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Miura, H., Takahashi, S., Shibata, T. et al. Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing. Nat Protoc 15, 4058–4100 (2020). https://doi.org/10.1038/s41596-020-0378-5

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