Role of the reprogramming factors in inducing pluripotency

Induced pluripotent stem (iPS) cells can be obtained from fibroblasts by expression of Oct4, Sox2, Klf4, and c-Myc. To determine how these factors induce this change in cell identity, we carried out genomewide promoter analysis of their binding in iPS and partially reprogrammed cells. Most targets in iPS cells are shared with ES cells and the factors cooperate to activate the ES-like expression program. In partially reprogrammed cells, genes bound by c-Myc have achieved a more ES-like binding and expression pattern. In contrast, genes that are co-bound by Oct4, Sox2, and Klf4 in ES cells and that encode pluripotency regulators show severe lack of both binding and transcriptional activation. Among the factors, c-Myc has a pivotal effect on the initiation of the ES transcription program, including the repression of fibroblast-specific genes. Our analysis begins to unravel how the four factors function together and suggests a temporal and separable order of their effects during reprogramming. For genome wide expression analysis: A. ES/iPS/partial iPS cells were analyzed in duplicates from 2 different cell lines (e.g four samples per cell type) B. tet inducible factors (tetO/tetS/tetC/tetK) were analyzed individually, a control was an uninduced tet line. C. OCK expression was performed in duplicate with 2 different clones. For genome wide location analysis (ChIP-chip): Oct4/Sox2/c-Myc/Klf4 were performed with biological duplicates (2 clonally isolated iPS/partial iPS lines and ES cells were performed with v6.5 and E14 cell lines)