Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin

Hirose, Kentaro; Shimoda, Nobuyoshi; Kikuchi, Yutaka

doi:10.4161/epi.25653

Cited by 38 publications

(33 citation statements)

References 28 publications

(53 reference statements)

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“…In accordance with the reduction of 5mC, we observed significant downregulation of DNMTs and the critical regulator of DNA methylation uhrf1, a factor that is associated with liver regeneration and redistribution of H3K27me3 from promoters to transposons [83]. Our results obtained at 6 hPR in t-rRPE, partially recapitulate the results observed during fin regeneration in zebrafish where the levels of 5mC and 5hmC were transiently reduced at 24 hours post-amputation (hpa) in the blastema cells, and such reduction was also independent of proliferation [37]. However, in the t-rRPE we did not detect significant changes in the levels of 5hmC evaluated by immunofluorescence staining and only small but significant upregulation of tet3 was observed at 24 hPR (Figure 2b).…”

Section: Discussionsupporting

confidence: 84%

“…For example, in the Xenopus froglet, DNA methylation affects the limb regenerative capacity mediated by an enhancer sequence named Mammalian Fish Conserved Sequence 1 (MFCS1) which controls the expression of Shh [34]. On the other hand, dynamic changes in DNA methylation and expression patterns of DNMTs have been observed during Müller glia (MG) reprogramming [35,36] and in zebrafish fin regeneration [37][38][39]. It has also been demonstrated that MG reprogramming, proliferation, and optic nerve regeneration are affected after knockdown (KD) of apobec2a and apobec2b-enzymes involved in deamination of methylated DNA [40].…”

Section: Introductionmentioning

confidence: 99%

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DNA demethylation is a driver for chick retina regeneration

Luz-Madrigal

Grajales-Esquivel

Tangeman

et al. 2019

Preprint

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ABSTRACTBackgroundA promising avenue toward human retina regeneration lies in identifying the factors that promote cellular reprogramming to retinal neurons in organisms able to undergo retina regeneration. The embryonic chick can regenerate a complete neural retina, after retinectomy, via retinal pigment epithelium (RPE) reprogramming in the presence of FGF2. Cellular reprogramming resets the epigenetic landscape to drive shifts in transcriptional programs and cell identity. Here, we systematically analyzed the reprogramming competent chick RPE prior to injury, and during different stages of reprogramming. We examined the dynamic changes in the levels and distribution of histone marks and DNA modifications, as well as conducted a comprehensive analysis of the DNA methylome during this process.ResultsIn addition to changes in the expression of genes associated with epigenetic modifications during RPE reprogramming, we observed dynamic changes in histone marks and intermediates of the process of DNA demethylation. At early times after injury, H3K27me3 and 5mC repression marks decreased while 5caC and the H3K4me3 activation mark increased, suggesting genome-wide changes in the bivalent chromatin, impaired DNA methylation, and active DNA demethylation in the chromatin reconfiguration of reprogramming RPE. Comprehensive analysis of the methylome by whole-genome bisulfite sequencing (WGBS) confirmed extensive rearrangements of DNA methylation patterns including differentially methylated regions (DMRs) found at promoters of genes associated with chromatin organization and fibroblast growth factor production. In contrast, genes associated with early RPE reprogramming are hypomethylated in the intact RPE and remain hypomethylated during the process. During the generation of a neuroepithelium (NE) at later stages of reprogramming, decreased levels of H3K27me3, 5mC, and 5hmC coincide with elevated levels of H3K27Ac and 5caC, indicating an active demethylation process and genome-wide changes in the active regulatory landscape. Finally, we identify Tet methylcytosine dioxygenase 3 (TET3) as an important factor for DNA demethylation and retina regeneration in the embryonic chick, capable of reprogramming RPE in the absence of exogenous FGF2.ConclusionOur results demonstrated that injury signals early in RPE reprogramming trigger genome-wide dynamic changes in chromatin, including bivalent chromatin and DNA methylation. In the presence of FGF2 these dynamic modifications are further sustained in the commitment to form a new retina. We identify DNA demethylation as a key process driving the process of RPE reprogramming and identified TET3 as a factor able to reprogram RPE in absence of FGF2. Our findings reveal active DNA demethylation as an important process that may be applied to remove the epigenetic barriers in order to regenerate retina in mammals.

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Section: Discussionsupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

DNA demethylation is a driver for chick retina regeneration

Luz-Madrigal

Grajales-Esquivel

Tangeman

et al. 2019

Preprint

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“…This topic has been recently investigated in the context of zebrafish caudal fin regeneration. Based on the assessment of 5‐methylcytosine and 5‐hydromethylcytosine, it has been proposed that the early phase of fin regeneration is characterized by a transient DNA demethylation and expression of DNA demethylation‐ and repair‐related genes (Hirose et al ). The study of Stewart et al () demonstrated that histone modifications at specific loci might be an important regulatory mechanism for the reactivation of a regeneration gene expression program and for the initiation of regeneration.…”

Section: Epigenetic Regulators Of Fin Regenerationmentioning

confidence: 99%

The art of fin regeneration in zebrafish

2015

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The zebrafish fin provides a valuable model to study the epimorphic type of regeneration, whereby the amputated part of the appendage is nearly perfectly replaced. To accomplish fin regeneration, two reciprocally interacting domains need to be established at the injury site, namely a wound epithelium and a blastema. The wound epithelium provides a supporting niche for the blastema, which contains mesenchyme‐derived progenitor cells for the regenerate. The fate of blastemal daughter cells depends on their relative position with respect to the fin margin. The apical compartment of the outgrowth maintains its undifferentiated character, whereas the proximal descendants of the blastema progressively switch from the proliferation program to the morphogenesis program. A delicate balance between self‐renewal and differentiation has to be continuously adjusted during the course of regeneration. This review summarizes the current knowledge about the cellular and molecular mechanisms of blastema formation, and discusses several studies related to the regulation of growth and morphogenesis during fin regeneration. A wide range of canonical signaling pathways has been implicated during the establishment and maintenance of the blastema. Epigenetic mechanisms play a crucial role in the regulation of cellular plasticity during the transition between differentiation states. Ion fluxes, gap‐junctional communication and protein phosphatase activity have been shown to coordinate proliferation and tissue patterning in the caudal fin. The identification of the downstream targets of the fin regeneration signals and the discovery of mechanisms integrating the variety of input pathways represent exciting future aims in this fascinating field of research.

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“…DNA methylation, an essential type of epigenetic modification, is crucial for the establishment and maintenance of cellular identity (Bird, 2002). The level of DNA methylation is correlated with differential gene expression among different tissue types, and there is increasing evidence that DNA methylation negatively influences gene expression during cellular proliferation (Wu and Zhang, 2010;Cedar and Bergman, 2012;Franchini et al, 2012), differentiation (Alvaro et al, 2007), genomic imprinting, and regeneration (Hirose et al, 2013;Takayama et al, 2014). For example, sonic hedgehog (shh) gene is hypomethylated in Xenopus tadpoles, which have the ability to regenerate missing limbs; in contrast shh is hypermethylated in Xenopus froglets, which are unable to regenerate lost appendages (Yakushiji et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Analysis of Genomewide DNA Methylation Reveals Differences in DNA Methylation Levels between Dormant and Naturally as well as Artificially Potentiated Pedicle Periosteum of Sika Deer (Cervus nippon)

et al. 2016

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Deer antlers are the only mammalian appendages that can fully regenerate each year from the permanent bony protuberances of the frontal bones, called pedicles. Pedicle periosteum (PP) is the key tissue for antler regeneration and the source of antler stem cells. The distal one third of the PP has acquired the ability to regenerate antlers and is termed the potentiated PP (PPP), whereas the proximal two thirds of the PP requires further interactions within its niche to launch antler regeneration and is termed the dormant PP (DPP). However, the molecular mechanisms underlying the process of potentiation from the DPP to the PPP are unknown. In this study, we used the fluorescence-labeled methylation-sensitive amplified polymorphism method to assess the levels of DNA methylation in both cells and tissues of the PPP and the DPP. The results showed that the levels of DNA methylation were significantly lower in the PPP compared to the DPP (P < 0.05). Therefore, DNA demethylation may be involved in the process of this potentiation. This involvement was further confirmed by functional testing by artificially creating a potentiated PP (aPPP) from DPP tissue. Moreover, we identified 15 methylated fragments by the methylation sensitive amplified polymorphism method that are either unique to the PPP or the DPP, which were further confirmed by Southern blot analysis. Taken together, our data suggest that DNA demethylation is involved in the process of PP potentiation, which is a prerequisite step for the initiation of antler regeneration. These findings provide the first experimental evidence to link epigenetic regulation and mammalian appendage regeneration.

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Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin

Cited by 38 publications

References 28 publications

DNA demethylation is a driver for chick retina regeneration

DNA demethylation is a driver for chick retina regeneration

The art of fin regeneration in zebrafish

Analysis of Genomewide DNA Methylation Reveals Differences in DNA Methylation Levels between Dormant and Naturally as well as Artificially Potentiated Pedicle Periosteum of Sika Deer (Cervus nippon)

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