GSE159410
Human transcription factors responsive to initial reprogramming are predominantly legitimate during iPSC reprogramming
The four transcription factors OCT4, SOX2, KLF4 and MYC (OSKM) together can convert human fibroblasts to induced pluripotent stem cells (iPSCs). It is, however, perplexing that they can do so only for a rare population of the starting cells with a long latency. Transcription factors (TFs) define identities of both the starting fibroblasts and the end product, iPSCs, and are of paramount importance for the reprogramming process as well. It is critical to upregulate or activate iPSC-enriched TFs while downregulate or silence the fibroblast-enriched TFs. This report explores the initial TF responses to OSKM as the molecular underpinnings for both the potency aspect and limitation sides of the OSKM reprogramming. The author first defined the TF reprogramome, i.e., the full complement of TFs to be reprogrammed. Most TFs were resistant to OSKM reprogramming at the initial stages, which agrees with the inefficiency and long latency of iPSC reprogramming. Surprisingly, the current analyses revealed that the majority of the TFs (83 genes) that did respond to OSKM induction underwent legitimate reprogramming. The initial legitimate transcriptional responses of TFs to OSKM reprogramming were observed from fibroblasts from a different individual.  Such early biased legitimate reprogramming of the responsive TFs aligns well with the robustness aspect of the otherwise inefficient and stochastic OSKM reprogramming Overall design: There are 19 RNA-seq in this deposit. We sequenced RNA from two human embryonic stem cell (ESC) lines, H1 and H9, each of which has two repeats. We have also sequenced two normal human fibroblast cell lines from different individuals  four technical repeasts for each cell line. We have also sequenced RNA from one fibroblasts transduced with the four reprogramming factors (OSKM), two of which were 48 hours post transduction and the other two were 72 hours post factor transduction. We additionally sequenced RNA from another fibroblast cell line transduced with OSKM, but the RNA samples were taken at 96 hours post transduction (three technical repeats).