Competency for shoot regeneration from Arabidopsis root explants is regulated by DNA methylation

Shemer, Or; Landau, Udi; Candela, Héctor; Zemach, Assaf; Williams, Leor Eshed

doi:10.1016/j.plantsci.2015.06.015

Cited by 66 publications

(40 citation statements)

References 79 publications

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“…A positive impact of auxin on the CMT3 expression has also been reported by others (Parizot et al 2010;Shemer et al 2015). In support of the auxin-controlled expression of CMT3 is the presence of the auxin-responsive motif, AuxRE, in the promoter of this gene (http://arabi dopsi s.med.ohio-state .edu/Atcis DB/), which implies that ARFs, the core elements of auxin signalling that are believed to play roles in SE induction in Arabidopsis (Weijers and Wagner 2016;Wójcikowska and Gaj 2017), might regulate CMT3 in response to auxin treatment.…”

Section: Both the Maintenance And De Novo Pathways Of Dna Methylationsupporting

confidence: 81%

“…The contrasting embryogenic capacity of the cmt3 and met1 mutants suggests that the contribution of the CMT3 and MET1 methylases to SE appears to be different. The role of CMT3 in the callus-mediated shoot regeneration of Arabidopsis (Shemer et al 2015) might suggest that in the SE system of Arabidopsis in which marginal callus production accompanies the direct development of somatic embryos from explant cells (Gaj 2001;Kurczyńska et al 2007), the function of CMT3 might be not critical for SE induction. In contrast, the importance of MET1 activity for SE induction might be related with the role of the enzyme in the hormone-related processes that play a central role in SE induction (Nic-Can and Loyola-Vargas 2016).…”

Section: Both the Maintenance And De Novo Pathways Of Dna Methylationmentioning

confidence: 99%

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Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

et al. 2018

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Epigenetic processes including DNA methylation play a pivotal role in regulating the genes that control plant development. In contrast to in planta development, the contribution of DNA methylation to the morphogenic processes that are induced in vitro are much less recognised. Hence, in the present study, we analysed the impact of DNA methylation on somatic embryogenesis (SE) that was induced in Arabidopsis. The results demonstrated a decrease in the global DNA methylation level during SE that contrasted with the up-regulation of MET1 and CMT3 DNA methylases and the down-regulation of DNA demethylases (ROS1, DME and DML2). Hence, the global DNA methylation level appears not to correlate with the transcriptional activity of the genes encoding DNA methylases/demethylases, thereby implying the complexity of the regulatory mechanism that controls the DNA methylation status of the SE-epigenome. Moreover, distinct changes in the expression level of the SE-regulatory genes were indicated in the 5-AzaC-treated and DNA methylase mutant cultures. Accordingly, a significant repression of the LEC2, LEC1 and BBM genes was found in the 5-AzaC-treated culture that was incapable of SE induction. In contrast, the distinct up-regulation of these genes was observed in the drm1drm2 and drm1drm2cmt3 mutant cultures with an improved embryogenic response. The modulated expression of DNA methylase genes and the significantly modified embryogenic response of the met1 and drm mutants imply that both the maintenance and the de novo pathway of DNA methylation are engaged in the regulation of SE in Arabidopsis.

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Section: Both the Maintenance And De Novo Pathways Of Dna Methylationsupporting

confidence: 81%

Section: Both the Maintenance And De Novo Pathways Of Dna Methylationmentioning

confidence: 99%

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

et al. 2018

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“…STM), WUS is not methylated in the competent lateral root and remains in that state throughout the early stages of conversion. Since methylation is generally associated with gene repression, an unmethylated WUS locus might reflect that the developing LRP is open to a change in identity, in this case induced by cytokinin (Li et al, 2011;Shemer et al, 2015). The hypothesis that switchable organs have a chromatin state favorable to conversion is further supported by the identification of genes similarly regulated during direct conversion (this report) and in hypomethylated mutants prone to shoot organogenesis (Li et al, 2011).…”

Section: What Locks Organ Identity?mentioning

confidence: 63%

“…Changes in DNA methylation occurring during conversion are not correlated with transcription modulation Mutants resulting in the functional loss of DNA methylation showed earlier and more efficient de novo shoot regeneration that correlated with hypomethylated regions in the WUS locus, and with earlier and higher WUS transcription than in wild type (Li et al, 2011;Shemer et al, 2015). We thus tested whether the large-scale changes in gene expression observed through the root-to-shoot conversion are linked with variations in DNA methylation across the nuclear genome.…”

Section: Direct Conversion Is a Transdifferentiation Processmentioning

confidence: 99%

Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development

et al. 2017

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To understand how the identity of an organ can be switched, we studied the transformation of lateral root primordia (LRP) into shoot meristems in Arabidopsis root segments. In this system, the cytokinininduced conversion does not involve the formation of callus-like structures. Detailed analysis showed that the conversion sequence starts with a mitotic pause and is concomitant with the differential expression of regulators of root and shoot development. The conversion requires the presence of apical stem cells, and only LRP at stages VI or VII can be switched. It is engaged as soon as cell divisions resume because their position and orientation differ in the converting organ compared with the undisturbed emerging LRP. By alternating auxin and cytokinin treatments, we showed that the root and shoot organogenetic programs are remarkably plastic, as the status of the same plant stem cell niche can be reversed repeatedly within a set developmental window. Thus, the networks at play in the meristem of a root can morph in the span of a couple of cell division cycles into those of a shoot, and back, through transdifferentiation.

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“…The genes and retrotransposon superfamilies Ty 1 ‐copia , Ty 3 ‐gypsy and env ‐like retrotransposons, and L1‐LINEs were more hypomethylated than hypermethylated in callus compared with leaves, consistent with the observed hypomethylation upon callus induction in rice and maize (Stroud et al ., ; Stelpflug et al ., ). Callus induction under tissue culture conditions coincides with the onset of dedifferentiation programs and alterations in the transcriptome (Sugimoto et al ., ) and might be partially due to cytosine hypomethylation of genes (Shemer et al ., ). In sugar beet callus, the hypomethylation of retrotransposons and DNA transposons might lead to genomic rearrangements or instability, known as somaclonal variation, upon tissue culture (Tanurdzic et al ., ).…”

Section: Discussionmentioning

confidence: 97%

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

et al. 2017

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The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H = A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves.

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Competency for shoot regeneration from Arabidopsis root explants is regulated by DNA methylation

Cited by 66 publications

References 79 publications

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

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