Conversion of genomic imprinting by reprogramming and redifferentiation

Abstract

SummaryInduced pluripotent stem cells (iPSCs), generated from somatic cells by overexpression of transcription factors Oct4, Sox2, Klf4 and cMyc have the same characteristics as pluripotent embryonic stem cells (ESCs). iPSCs reprogrammed from differentiated cells undergo epigenetic modification during reprogramming, and ultimately acquire a similar epigenetic state to that of ESCs. In this study, these epigenetic changes were observed in reprogramming of uniparental parthenogenetic somatic cells. The parthenogenetic pattern of imprinted genes changes during the generation of parthenogenetic maternal iPSCs (miPSCs), a process referred to as pluripotent reprogramming. We determined whether altered imprinted genes are maintained or revert to the parthenogenetic state when the reprogrammed cells are redifferentiated into specialized cell types. To address this question, we redifferentiated miPSCs into neural stem cells (miPS-NSCs) and compared them with biparental female NSCs (fNSCs) and parthenogenetic NSCs (pNSCs). We found that pluripotent reprogramming of parthenogenetic somatic cells could reset parthenogenetic DNA methylation patterns in imprinted genes, and that alterations in DNA methylation were maintained even after miPSCs were redifferentiated into miPS-NSCs. Notably, maternally methylated imprinted genes (Peg1, Peg3, Igf2r, Snrpn and Ndn), whose differentially methylated regions were fully methylated in pNSCs, were demethylated and their expression levels were found to be close to the levels in normal biparental fNSCs after reprogramming and redifferentiation. Our findings suggest that pluripotent reprogramming of parthenogenetic somatic cells followed by redifferentiation leads to changes in DNA methylation of imprinted genes and the reestablishment of gene expression levels to those of normal biparental cells.

Epigenetic alteration of imprinted genes during neural differentiation of germline-derived pluripotent stem cells

“…Alteration of the uniparental imprinting status in Ndn was previously reported by Kim et al (2013), who found a loss of DNA methylation during induction of pluripotency in parthenogenetic NSCs. Ndn plays an important role in proliferation and apoptosis of NSCs and in neuronal development and terminally differentiated neurons.…”

“…S2). 8 Mest hypermethylation has been previously described in ESCs. 9 The aberrant methylation of imprinted genes like Mest in ESCs and ES-NSCs can be readily detected in human ESCs.…”

“Epigenetic Memory” Phenomenon in Induced Pluripotent Stem Cells

“…This fact is supported by the results of another study with iPSCs from neutral stem cells isolated from a partenogenetic mouse embryo. In these cells, the expression levels of the cells with paternal imprinting, Peg1 (or Mest ), Ndn and Snurf determined using microchips, was much lower than those in somatic cells from the embryos obtained by normal biparental fertilization, since these genes were reactivated during reprogramming [27]. Thus, the epigenetic memory phenomenon has a real impact on iPSC characteristics, and the consequences of its presence may be serious.…”

Reactivation of inactive X chromosome and post-transcriptional reprogramming of Xist in induced pluripotent stem cells

“…Among the various pluripotent cell types, iPSCs are the most similar to embryonic stem cells (ESCs), based on their molecular signature and differentiation potential, and they fulfill all the criteria for pluripotency -the formation of germline-competent chimeras (Okita et al, 2007), germline transmission (Kim et al, 2008;Shi et al, 2008) and full-term development after tetraploid complementation (Kang et al, 2009;Zhao et al, 2009). The generation of iPSCs also entails epigenetic modification, such as changes in genomic imprinting (Kim et al, 2013), histone modification (Maherali et al, 2007) and reactivation of the inactive X chromosome (Xi) (Maherali et al, 2007;Ohhata and Wutz, 2013). Generally, the efficiency of iPSC derivation using four transcription factors varies depending on the origin of the somatic cells, and ranges from 0.01 to 3.6% (Takahashi and Yamanaka, 2006;Maherali et al, 2007;Okita et al, 2007;Wernig et al, 2007;Huangfu et al, 2008;Kim et al, 2008).…”