A single-cell multiomics approach for simultaneous analysis of replication timing and gene expression

Replication timing (RT) allows us to analyze temporal patterns of genome-wide replication, that is, if genes replicate early or late during the S-phase of the cell cycle. RT has been linked to gene expression in normal and diseased acute and chronic states, such as cancer. However, studies done to date focused on bulk cell populations that required tens of thousands of cells for RT analysis. Here, we developed an affordable novel single-cell (sc) multiomics approach to simultaneously analyze RT and gene expression from cells or nuclei. We used this approach to generate single-cell RT profiles and sc-gene expression data from the well-established human liver cancer cell line, HepG2. We demonstrated that as few as 17 mid S-phase cells were sufficient to produce cell type-specific pseudo bulk RT profiles that had a high correlation to previously published HepG2 bulk RT profiles. The single-cell RT profiles allowed us to visualize how individual cells progressed through genome replication. We were also able to demonstrate cell-specific correlations between RT and gene expression, which to our knowledge, has not been reported. We observed trends that were conserved between individual cells, as well as cell-to-cell variations, which were not possible to detect with the bulk RT studies.