Chemically-induced DNA de-methylation alters the effectiveness of microspore embryogenesis in triticale

Nowicka, Anna; Juzoń, Katarzyna; Krzewska, Monika; Dziurka, Michał; Dubas, Ewa; Kopeć, Przemysław; Zieliński, Kamil; Żur, Iwona

doi:10.1016/j.plantsci.2019.110189

Cited by 20 publications

(27 citation statements)

References 52 publications

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“…The most commonly used inhibitors in the plant field are the non‐methylable cytidine analogs 5‐azacytidine (AC) and zebularine (Zeb), the methyl group synthesis inhibitor 3‐deazaneplanocin A (DZNep) and the histone deacetylase class I and II inhibitor trichostatin A (TSA). Epigenetic inhibitors were instrumental in understanding the dynamics of DNA methylation and transposon silencing in A. thaliana , Nicotiana tabacum and cereals (Fajkus et al , ; Fojtová et al , ; Kovarik et al , ; Griffin et al , ), understanding the mechanisms of establishment and maintenance of DNA methylation (Baubec et al , , ) and altering the plant developmental program (Fulneček et al , ; Solís et al , ; Nowicka et al , ). In addition, there are reports from prokaryotes, fungi, animals and plants that specific epigenetic inhibitors cause genomic instability (Zadražil et al , ; Fučík et al , ; Hegde et al , ; Kiziltepe et al , ; Kuo et al , ; Cho et al , ; Orta et al , ; Liu et al , ).…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage

et al. 2019

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Repetitive DNA sequences and some genes are epigenetically repressed by transcriptional gene silencing (TGS). When genetic mutants are not available or problematic to use, TGS can be suppressed by chemical inhibitors. However, informed use of epigenetic inhibitors is partially hampered by the absence of any systematic comparison. In addition, there is emerging evidence that epigenetic inhibitors cause genomic instability, but the nature of this damage and its repair remain unclear. To bridge these gaps, we compared the effects of 5-azacytidine (AC), 2 0 -deoxy-5-azacytidine (DAC), zebularine and 3-deazaneplanocin A (DZNep) on TGS and DNA damage repair. The most effective inhibitor of TGS was DAC, followed by DZNep, zebularine and AC. We confirmed that all inhibitors induce DNA damage and suggest that this damage is repaired by multiple pathways with a critical role of homologous recombination and of the SMC5/6 complex. A strong positive link between the degree of cytidine analog-induced DNA demethylation and the amount of DNA damage suggests that DNA damage is an integral part of cytidine analog-induced DNA demethylation. This helps us to understand the function of DNA methylation in plants and opens the possibility of using epigenetic inhibitors in biotechnology.

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Section: Introductionmentioning

confidence: 99%

Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage

et al. 2019

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“…Our study has demonstrated that the asymmetric division is followed by global repression of genes associated with cell pluripotency and somatic development (Liu et al ., 2018). Several evidence lines have shown that decreased DNA methylation might promote the microspore's embryogenesis initiation in Brassica and triticale (Solís et al ., 2012, 2015; Nowicka et al ., 2019). Tomato microspores showed similar DNA methylome with leaves, and they both can be induced for plant regeneration (Segui‐Simarro and Nuez, 2007; Cruz‐Mendívil et al ., 2011).…”

Section: Discussionmentioning

confidence: 99%

DNA methylation dynamics of sperm cell lineage development in tomato

Song

Liu

et al. 2020

The Plant Journal

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SUMMARY During the sexual reproduction of higher plants, DNA methylation and transcription are broadly changed to reshape a microspore into two sperm cells (SCs) and a vegetative cell (VC). However, when and how the DNA methylation of SCs is established remains not fully understood. Here we investigate the DNA methylation (5 mC) dynamics of SC lineage and the VC in tomato using whole‐genome bisulfite sequencing. We find the asymmetric division of the microspore gives its two daughter cells differential methylome. Compared with the generative cell (GC), the VC is hypomethylated at CG sites while hypermethylated at CHG and CHH sites, with the majority of differentially methylation regions targeted to transposable elements (TEs). SCs have a nearly identical DNA methylome to the GC, suggesting that the methylation landscape in SCs may be pre‐established following the asymmetric division or inherited from the GC. The random forest classifier for predicting gene and TE expression shows that methylation within the gene body is a more powerful predictor for gene expression. Among all tested samples, gene and TE expression in the microspore may be more predictable by DNA methylation. Our results depict an intact DNA methylome landscape of SC lineage in higher plants, and reveal that the impact of DNA methylation on transcription is variant in different cell types.

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“…Currently, DNA demethylating compounds that can de-repress the expression of the genes with hypermethylated promoters have wider applications. The most common applications are in tissue cultures, where 5-AzaC treatment has a beneficial effect on the induction of somatic embryogenesis [ 124 , 125 , 126 ], microspore embryogenesis [ 127 , 128 ], and shoot regeneration [ 129 ]. Another study has taken advantage of the fact that flowering is controlled by, amongst other things, DNA methylation [ 130 ].…”

Section: Epigenetic Advances In Crop Improvement: Exploiting Epigenetic Diversitymentioning

confidence: 99%

Epigenetics for Crop Improvement in Times of Global Change

Kakoulidou

Avramidou²,

Baránek

et al. 2021

Biology

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Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity—naturally, genetically, chemically, or environmentally induced—can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.

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Chemically-induced DNA de-methylation alters the effectiveness of microspore embryogenesis in triticale

Cited by 20 publications

References 52 publications

Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage

Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage

DNA methylation dynamics of sperm cell lineage development in tomato

Epigenetics for Crop Improvement in Times of Global Change

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