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At Florida State University, we have developed a method to identify sets of regions that replicate at unique times in any given cell type.
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Background: At Florida State University, we have developed a method to identify sets of regions that replicate at unique times in any given cell type (replication timing fingerprints) using pluripotent stem cells as an example, and show that genes in the pluripotency fingerprint belong to a class previously shown to be resistant to reprogramming in induced pluripotent stem cells (iPSCs), identifying potential new target genes for more efficient iPSC production. We propose that the order in which DNA is replicated (replication timing) provides a novel means for classifying cell types, and can reveal cell type specific features of genome organization. A major advantage of our fingerprinting method is in selection of a minimal set of regions that allow for classification with a straightforward PCR-based timing assay and a reasonably small set of primers, particularly if only cell-type specific regions are examined. Our results suggest that a standard set of 20 fingerprint loci can be effective for classification, but the number of regions queried can be adjusted based on the confidence level required. The sole requirement for replication profiling is the collection of a sufficient number of proliferating cells for sorting on a flow cytometer. Consistently, just as replication fingerprints can be generated for particular cell types or general categories of cells, features of replication profiles allow for the creation of disease-specific fingerprints, which may be valuable for prognosis. We have also identified regions that may undergo important organizational changes upon differentiation.