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bioRxiv · 10.1101/237628

Genome-wide stability of the DNA replication program in single mammalian cells

Takahashi, S.·Miura, H.·Shibata, T.·Nagao, K.·Okumura, K.·Ogata, M.·Obuse, C.·Takebayashi, S.-i.·Hiratani, I.
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Abstract

Here, we report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.

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Takahashi, S., Miura, H., Shibata, T., Nagao, K., Okumura, K., Ogata, M., Obuse, C., Takebayashi, S.-i., Hiratani, I.. 2017-12-25. Genome-wide stability of the DNA replication program in single mammalian cells. https://doi.org/10.1101/237628

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