Comparative genomic analysis focused on early and intermediate phases of cellular reprogramming

Mechanistic interpretation of the reprogramming process is still remained elusive. Thus, we compared two reprogramming processes, pluripotent cell-specific factor-mediated direct reprogramming (PDR) and induced pluripotent stem cells reprogramming (iPSCR), to figure out how and when these processes are bifurcated from each other during the reprogramming. Until day 6, all samples showed a similar pattern of gene expression, but the pattern has changed dramatically after day 6 regardless of dox-induction or specific cues for cell fate determination. These suggest that the process of PDR also can be divided into two stages, early and late. We assume that around day 6 is intermediate stage which is not clearly defined but to be epigenetically flexible as in iPSCR. When we focused on the increased genes during early phase of reprogramming, we found these genes could be divided into five distinct groups by the expression pattern during whole reprogramming process. Interestingly, one of the groups showed exclusively up-regulated pattern on day 4 or 6 but down-regulated afterwards in all analyzed samples. Thus, we assumed that this group of genes are highly related to the cells in intermediate stage (IC). Gene Ontology analysis shows that these IC-genes are majorly involved in epidermis development and retinoic acid metabolism. We expect that study on the roles of these genes provides mechanistic understanding of the early and intermediate stages of cellular reprogramming. Time series design with samples during iPSCR and PDR of 2'MEF and 4F2A MEF