Novel approaches to map DNA replication traffic in a genome-wide scale

PROJECT SUMMARY The overarching goal of the project is to establish novel genomics and bioinformatics approaches to model patterns of DNA replication in cells. It is known that the patterns of DNA replication are intimately linked to the cell type. These differences between cell types are relevant to the integrity of the genome during cell type transitions. For example, we recently found that damage during DNA replication is increased during the induced transition from one cell type to another. However, there is a lack of methodology to observe replication patterns in human cells. DNA replication differs between different cell types in the location of initiation, the direction of fork progression, and the timing of initiation and completion. There is currently no method that can comprehensively map the progression of DNA replication to the genome. Because of the importance of DNA replication in cell proliferation, there is need for the development of such methods. To be able to examine the progression of DNA polymerases in human cells, we will develop a novel methodology to map DNA replication genome-wide, by incorporating nucleotide analogs during DNA replication, and sequencing the resulting DNA molecules by Nanopore sequencing and recording the electrical signals. In parallel, we will develop novel bioinformatics approaches to reliably examine the electrical signals and identify bases or regions of DNA replication, for comparison between different cell types, or between healthy and diseased tissues. Successful establishment of this technology will greatly increase our knowledge of replication, genetic stability and cell proliferation, and allow the community to characterize differences in the progression of DNA replication between cell types.