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

Nat Genet. 2019 Mar;51(3):529-540. doi: 10.1038/s41588-019-0347-5. Epub 2019 Feb 25.


Here, we report a single-cell DNA replication sequencing method, scRepli-seq, a 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 profiles, which were also conserved among cells. Haplotype-resolved scRepli-seq revealed similar replication 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, which was smallest at the beginning and the end of S phase. In addition, developmentally regulated domains were found to deviate from others and showed a higher degree of heterogeneity, thus suggesting a link to developmental plasticity. Moreover, allelic expression imbalance was found to strongly associate with replication-timing asynchrony. Our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into three-dimensional genome organization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation / genetics
  • Cell Line
  • DNA / genetics*
  • DNA Copy Number Variations / genetics
  • DNA Replication / genetics*
  • DNA Replication Timing / genetics
  • Embryonic Stem Cells / physiology
  • Genome / genetics
  • Genome-Wide Association Study / methods
  • Genomic Instability / genetics
  • Humans
  • Mammals / genetics*
  • Mice
  • Mouse Embryonic Stem Cells / physiology
  • S Phase / genetics
  • X Chromosome / genetics


  • DNA