GSE60627
Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells
We investigated genome-wide nucleosome coverage and histone methylation occupancies in somatic MEFs, intermediate pre-iPSCs and fully reprogrammed iPSCs. We found that nucleosome occupancies increased in promoter regions and decreased in intergenic regions in pre-iPSCs and then recover to an intermediate level in iPSCs. Nucleosomes in pre-iPSCs are much more phased than those in MEFs and iPSCs. Bivalent, active, repressive domains are cell type-specific and change dynamically during reprogramming. HCG and LCG promoters exhibit distinct nucleosome occupancy patterns and are dynamically marked by H3K4me3/H3K27me3 during reprogramming, correspondingly showing different gene activities. Surprisingly, Vitamin C promotes nucleosome reorganization from pre-iPSCs to iPSCs. CTCF binding sites change dynamically during reprogramming, though they share a conserved binding motif. Nucleosome occupies CTCF sites to a higher extent in pre-iPSCs than those in MEFs and iPSCs. Taken together, our study reveals that dynamic changes of nucleosome positioning and chromatin organization associated gene regulation during reprogramming. Overall design: Examine dynamics of nucleosome positioning and histone modification profiles as well as gene expression regulation during somatic cell reprogramming