Kronos scRT: a uniform framework for single-cell replication timing analysis

A scalable approach to explore DNA replication in single cells reveals that although aneuploidy does not have a major impact on the pattern of replication, different cell types and sub-populations display distinguished replication paths. Mammalian genomes are replicated in a cell type-specific order and in coordination with transcription and chromatin organization. Currently, single-cell replication studies require individual processing of sorted cells, yielding a limited number (<100) of cells. Here, we develop Kronos scRT, a software for single-cell Replication Timing (scRT) analysis. Kronos scRT does not require a specific platform or cell sorting, which allows investigating large datasets obtained from asynchronous cells. By applying our tool to published data as well as droplet-based single-cell whole-genome sequencing data generated in this study, we exploit scRT from thousands of cells for different mouse and human cell lines. Our results demonstrate that although genomic regions are frequently replicated around their population average RT, replication can occur stochastically throughout S phase. Altogether, Kronos scRT allows fast and comprehensive investigations of the RT programme at the single-cell resolution for both homogeneous and heterogeneous cell populations.

Automated summary

The researchers developed Kronos scRT, a software for analyzing single-cell Replication Timing (scRT). By applying this tool to large datasets, they found that aneuploidy has a minor impact on replication patterns, but different cell types and sub-populations exhibit distinct replication paths.