ABSTRACT: Results from expression arrays identified that whole cultures of i12F-reprogrammed fibroblasts clustered in a defined group and indicated a switch in their genetic expression program, as shown by the significant up-regulation of 342 genes and the down-regulation of 288 genes in treated cells compared to MOCK controls. Manually isolated i12F clumps also clustered in a defined group different to i12F and showed significant up-regulation of 329 genes (193 of them shared with i12F treatment) and down-regulation of 372 genes (225 of them shared with i12F treatment) compared to MOCK controls (Fig. 1B). Functional enrichment analysis of the list of differentially regulated genes in i12F indicated their implication in germ cell-related processes such as “Integrin cell surface interactions” (REACT_13552), “Cell cycle” (REACT_152), “DNA Replication” (REACT_383), “Telomere maintenance (REACT_7970), as well as several Gene Ontology biological processes related to “Positive regulation of MAP kinase activity” (GO:0043406), “ovarian follicle development” (GO:0001541), “positive regulation of tyrosine phosphorylation of STAT protein” (GO:0042531), “Retinoid acid metabolic process” (GO:0042573) and “transforming growth factor beta receptor signaling pathway” (GO:0007179), among others. Interestingly, we observed the significant down-regulation of several genes related to the mitotic cell cycle regulation such as CDC45L, RRM2, CDKL2, CENPM, CENPP, ZWINT, PRKAR2B, PKMYT1, SKA3, ADORA2B, CDCA8, CDC6, BUB1 and LIG1, and the significant up-regulation of genes related to the TGFβ and LIF/STAT3 pathways such as INHBA, IL6, CSF2 and MAFB, and cell attachment to basal layer such as ITGA1, MMP9 and MMP10. On the other hand, we observed a specific significant down-regulation in the CLUMPS of several genes related to chromatin stability such as the linker histone 1 subunits H4B, H4H, H4K, H2AB and H3J, the core histone 2 subunits H2AA4 and H4B, and several somatic lineage determinant factors such as GATA2, NEUROD2 and SOX17. Aditionally we observed a significant up-regulation of extracellular matrix related genes such as ADAM8 and MMP14, and the pathway of LIF/STAT3
