Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers

Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers

BMC Biology, December 2014

25528259

Yu Tao, Weisheng Zheng, Yonghua Jiang, Guitao Ding, Xinfeng Hou, Yitao Tang, Yueying Li, Shuai Gao, Gang Chang, Xiaobai Zhang, Wenqiang Liu, Xiaochen Kou, Hong Wang, Cizhong Jiang, Shaorong Gao

BackgroundNucleosome organization determines the chromatin state, which in turn controls gene expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it is still unclear to what degree the re-established nucleosome organization of induced pluripotent stem cells (iPSCs) resembles embryonic stem cells (ESCs), and whether the iPSCs inherit some residual gene expression from the parental fibroblast cells.ResultsWe generated genome-wide nucleosome maps in mouse ESCs and in iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system. Pairwise comparisons showed that the nucleosome organizations in the iPSCs, regardless of the iPSCs¿ tissue of origin, were nearly identical to the ESCs, but distinct to mouse embryonic fibroblasts (MEF). There is a canonical nucleosome arrangement of -1, nucleosome depletion region, +1, +2, +3, et al. nucleosomes around the transcription start sites of active genes whereas only a nucleosome occupies at silent transcriptional units. Transcription factor binding sites possessed characteristic nucleosomal architecture such that their access was governed by the rotational and translational settings of the nucleosome. Interestingly, the tissue-specific genes were highly expressed only in the parental somatic cells of the corresponding iPS cell line before reprogramming, but had a similar expression level in the all resultant iPSCs and ESCs.ConclusionsThe re-established nucleosome landscape during nuclear reprogramming provides a conserved setting for accessibility of DNA sequences in mouse pluripotent stem cells. No persistent residual expression program or nucleosome positioning of the parental somatic cells that reflected their tissue of origin were passed onto the resulting mouse iPSCs.