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

Abstract

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 from mouse embryonic fibroblasts (MEF). There is a canonical nucleosome arrangement of -1, nucleosome depletion region, +1, +2, +3, and so on nucleosomes around the transcription start sites of active genes whereas only a nucleosome occupies 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 all the 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 was passed on to the resulting mouse iPSCs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-014-0109-x) contains supplementary material, which is available to authorized users.

Dynamic Reorganization of Nucleosome Positioning in Somatic Cells after Transfer into Porcine Enucleated Oocytes

“…In contrast, mouse pluripotent cells generated through SCNT did not appear to show such memories. However, in this study we found that the chromosomes in SCNT embryos and FZ both tended toward nucleosome loss and more open chromatin architecture within a few hours of reprogramming, especially in the X chromosome; similar changes occur in iPSC reprogramming (Tao et al., 2014, Huang et al., 2015). …”

Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells

“…Key epigenetic modifications of chromatin structure include the positioning of nucleosomes and covalent modifications to histone tails, which regulate the expression of specific genes 7 8 9 . Global maps of nucleosome positions in C. elegans 10 S. cerevisiae 11 12 and humans 13 14 show that nucleosomes are not randomly distributed throughout the genome but are highly organized, particularly at TSSs. Critically, dynamic changes of nucleosome positions have also been observed during the differentiation of mouse ESCs to neural progenitors 15 .…”

Genome-scale identification of nucleosome organization by using 1000 porcine oocytes at different developmental stages

“…A pair reads was treated as a fragment. The fragments were counted and then normalized as fragments (number of fragments in special region) per kilobase per million (FPKM) to calculate the nucleosome occupancy level [28, 29]. For each chromosome, nucleosome fragments were binned in 10-kb intervals.…”

“…Nucleosomes within 1 kb of the TSS were collected. The total 2-kb length was binned in 10-bp intervals, and the RPKM value in each bin was calculated to get a profile of nucleosome distribution around the TSS [29]. …”