Dynamics of transcription factor targeting and chromatin states during reprogramming

Induced pluripotent stem cells (iPSCs) have been produced from a number of mouse and human somatic cell types, upon the enforced expression of the transcription factors (TFs) Oct4, Klf4, Sox2, and c-Myc (OKSM). Reprogramming leads to inactivation of the somatic cell program and activation of the embryonic stem (ES) cell-specific program for self-renewal and pluripotency. Cells undergoing reprogramming initially downregulate the fibroblast-associated marker Thy1, then activate the Ssea1 marker. However only Ssea1+ cells can form iPSCs and Thy1+ and Thy1- cells are refractory cells. I firstly find why some cells are refractory and how the refractory cells can be rescued. Next an efficient reprogramming mouse model generates. Then both the spatial and temporal binding properties of these transcription factors during reprogramming investigates using Chromatin Immunoprecipitation, followed by qPCR which showed different binding patterns during reprogramming. I also investigates the compaction and protection of chromatin by DNase-MLPA and ATAC- seq across the different cell populations. Finally we studied the correlation among the TF binding, chromatin changes, nucleosomes shifting and transcriptional activity. The results of this study will further our understanding of transcriptional regulation by OKSM and how gene regulatory networks transpire during cellular reprogrammin