Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation and Hydroxymethylation in Reprogramming

Gao, Yawei; Chen, Jiayu; Li, Ké; Wu, Tong; Huang, Bo; Liu, Wenqiang; Kou, Xiaochen; Zhang, Yu; Huang, Hua; Jiang, Yonghua; Yao, Chao‐Ling; Liu, Xiaolei; Lü, Zhiwei; Xu, Zijian; Kang, Lan; Chen, Jun; Wang, Hailin; Cai, Tao; Gao, Shaorong

doi:10.1016/j.stem.2013.02.005

Cited by 325 publications

(334 citation statements)

References 51 publications

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“…Indeed, miR26a has been shown to promote myogenic (40,41) and neuronal (42) cell differentiation, although the involvement of TET and TDG in these processes awaits further investigation. Down-regulation of TET1 is known to be required for embryonic stem cell differentiation (2), whereas overexpression of TET1 can mimic Oct4 and help dedifferentiate fibroblasts into pluripotent stem cells (43). These results suggest an important role of TET/TDG-dependent DNA demethylation in maintenance of cell identity.…”

Section: Discussionmentioning

confidence: 97%

MicroRNA-26a targets ten eleven translocation enzymes and is regulated during pancreatic cell differentiation

Jin

Wang

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

125

115

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Ten eleven translocation (TET) enzymes (TET1/TET2/TET3) and thymine DNA glycosylase (TDG) play crucial roles in early embryonic and germ cell development by mediating DNA demethylation. However, the molecular mechanisms that regulate TETs/TDG expression and their role in cellular differentiation, including that of the pancreas, are not known. Here, we report that (i) TET1/2/3 and TDG can be direct targets of the microRNA miR-26a, (ii) murine TETs, especially TET2 and TDG, are down-regulated in islets during postnatal differentiation, whereas miR-26a is up-regulated, (iii) changes in 5-hydroxymethylcytosine accompany changes in TET mRNA levels, (iv) these changes in mRNA and 5-hydroxymethylcytosine are also seen in an in vitro differentiation system initiated with FACS-sorted adult ductal progenitor-like cells, and (v) overexpression of miR-26a in mice increases postnatal islet cell number in vivo and endocrine/acinar colonies in vitro. These results establish a previously unknown link between miRNAs and TET expression levels, and suggest a potential role for miR-26a and TET family proteins in pancreatic cell differentiation.T en eleven translocation (TET) enzymes and thymine DNA glycosylase (TDG) are implicated in active DNA demethylation (1-3). The three TET family enzymes oxidize 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), and subsequently to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) (1, 2, 4, 5). TDG, a base excision repair glycosylase, replaces 5fC and 5caC with an unmodified cytosine via DNA repair (5, 6). Despite these advances, the molecular mechanisms underlying TETs/ TDG regulation are still not known. In addition, although recent data suggest a role of TET and 5hmC in embryonic stem cells and primordial germ cells (2, 7-12), evidence for enzymatic demethylation by TET enzymes during differentiation of cells of later stages, such as the postnatal and adult stem cells of various organs including pancreas, remains very limited (13-16).MicroRNAs (miRNAs) are an abundant class of small, highly conserved noncoding RNAs that bind the 3′-untranslated regions (UTRs) of protein-coding genes to suppress gene expression. Accumulating data have demonstrated that miRNAs are critical for many developmental and cellular processes, including organogenesis and differentiation (17). However, the role of miRNAs in TET expression and active DNA demethylation remains unclear.Three major cell lineages exist in the adult pancreas-duct, acinar, and endocrine cells. The endocrine pancreas is composed of several hormone-releasing cells, including the insulin-secreting beta cells and glucagon-secreting alpha cells. Many transcription factors are known to control pancreas development (18). For example, the expression of pancreatic and duodenal homeobox 1 (Pdx1) in embryonic foregut region induces pancreas commitment (19,20), and those early progenitor cells have the potential to give rise to all three pancreatic lineages (21,22). Subsequent activation of another transcription factor, neurogenin 3 (N...

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Section: Discussionmentioning

confidence: 97%

MicroRNA-26a targets ten eleven translocation enzymes and is regulated during pancreatic cell differentiation

Jin

Wang

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

125

115

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“…By screening diverse factors that are normally expressed in pluripotent stem cells (PSCs), but not fibroblasts, for their ability to convert fibroblasts to pluripotency, the transcription factors Oct3/4, Sox2, Klf4, and c-Myc (O, S, K, and M) were found to trigger endogenous expression of pluripotent factors and be sufficient to reprogram fibroblasts into induced PSCs (iPSCs) (Takahashi and Yamanaka 2006). Although alternative sets of transcription factors for iPSC reprogramming have been reported (e.g., Buganim et al 2014), most studies include Oct3/4 and/or Sox2 (Yu et al 2007;Feng et al 2009;Han et al 2010;Gao et al 2013). How does this set of factors first interact with their target sites to initiate reprogramming?…”

Section: Pioneer Factors In Cell Reprogrammingmentioning

confidence: 99%

Pioneer transcription factors in cell reprogramming

2014

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A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in ''closed'' chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as ''pioneer factors'' to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.Cell fate control represents the most extreme form of gene regulation. Genes specific to the function of a particular type of cell may be antagonistic to the function of another type of cell, so nature has evolved diverse regulatory mechanisms to ensure stable patterns of gene activation and repression. In prokaryotes, self-sustaining regulatory networks of transcription factors bound to DNA can be sufficient to regulate gene activation and repression (Ptashne 2011). In eukaryotes, ;200-base-pair (bp) segments of the genome are wound nearly twice around an octamer of the four core histones to form nucleosomes, providing steric constraints on how transcription factors can bind DNA (Kornberg and Lorch 1999). As described below, pioneer transcription factors have the special property of being able to overcome such constraints, enabling the factors to engage closed chromatin that is not accessible by other types of transcription factors (Fig. 1). However, further higher-order packaging of nucleosomes into heterochromatin can occlude access to DNA altogether, presenting an additional barrier to cell fate conversion (Fig. 1). This review focuses on the most recent studies of pioneer factors in cell programming and reprogramming, how pioneer factors have special chromatinbinding properties, and facilitators and impediments to chromatin binding. We project that such knowledge will greatly aid future efforts to change the fates of cells at will for research, diagnostic, and therapeutic purposes.

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“…TET proteins can contribute to locus-specific demethylation in nESCs (1,14), and their depletion reduces the expression of pluripotency genes and increases methylation at their promoters (12,15). Furthermore, forced expression of TET1 and TET2 dramatically enhances iPSC reprogramming in a catalytically dependent manner (16)(17)(18). Nevertheless, the molecular signals that control TET activity in nESCs, and how they can be manipulated during reprogramming, are poorly characterized.…”

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confidence: 99%

Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms

Hore

Meyenn

Ravichandran

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

151

139

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Epigenetic memory, in particular DNA methylation, is established during development in differentiating cells and must be erased to create naïve (induced) pluripotent stem cells. The ten-eleven translocation (TET) enzymes can catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives, thereby actively removing this memory. Nevertheless, the mechanism by which the TET enzymes are regulated, and the extent to which they can be manipulated, are poorly understood. Here we report that retinoic acid (RA) or retinol (vitamin A) and ascorbate (vitamin C) act as modulators of TET levels and activity. RA or retinol enhances 5hmC production in naïve embryonic stem cells by activation of TET2 and TET3 transcription, whereas ascorbate potentiates TET activity and 5hmC production through enhanced Fe 2+ recycling, and not as a cofactor as reported previously. We find that both ascorbate and RA or retinol promote the derivation of induced pluripotent stem cells synergistically and enhance the erasure of epigenetic memory. This mechanistic insight has significance for the development of cell treatments for regenenerative medicine, and enhances our understanding of how intrinsic and extrinsic signals shape the epigenome.

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Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation and Hydroxymethylation in Reprogramming

Cited by 325 publications

References 51 publications

MicroRNA-26a targets ten eleven translocation enzymes and is regulated during pancreatic cell differentiation

MicroRNA-26a targets ten eleven translocation enzymes and is regulated during pancreatic cell differentiation

Pioneer transcription factors in cell reprogramming

Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms

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