Epigenetic Regulation of Phase Transitions in Arabidopsis thaliana

Trindade, Inês; Schubert, Daniel; Gaudin, Valérie

doi:10.1007/978-3-319-55520-1_18

Cited by 6 publications

(12 citation statements)

References 157 publications

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“…It is in line with other published results, indicating that mutually antagonistic bivalent histone marks, H3K4me2/3 and H3K27me3, have to be tightly balanced even at the same locus ( Du et al, 2013 ; Trindade et al, 2017 ).…”

Section: Discussionsupporting

confidence: 93%

BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans

et al. 2018

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In this paper we analyzed β-aminobutyric acid (BABA)-primed epigenetic adjustment of potato cv. “Sarpo Mira” to Phytophthora infestans. The first stress-free generation of the potato genotype obtained from BABA-primed parent plants via tubers and seeds showed pronounced resistance to the pathogen, which was tuned with the transcriptional memory of SA-responsive genes. During the early priming phase before the triggering stress, we found robust bistable deposition of histone marks (H3K4me2 and H3K27me3) on the NPR1 (Non-expressor of PR genes) and the SNI1 gene (Suppressor of NPR1, Inducible), in which transcription antagonized silencing. Switchable chromatin states of these adverse systemic acquired resistance (SAR) regulators probably reprogrammed responsiveness of the PR1 and PR2 genes and contributed to stress imprinting. The elevated levels of heritable H3K4me2 tag in the absence of transcription on SA-dependent genes in BABA-primed (F0) and its vegetative and generative progeny (F1) before pathogen challenge provided evidence for the epigenetic mark for intergenerational memory in potato. Moreover, our study revealed that histone acetylation was not critical for maintaining BABA-primed defense information until the plants were triggered with the virulent pathogen when rapid and boosted PRs gene expression probably required histone acetyltransferase (HAT) activity both in F0 and F1 progeny.

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Section: Discussionsupporting

confidence: 93%

BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans

et al. 2018

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“…Cytosine methylation, which is an epigenetic modification that activates or silences gene transcription to regulate multiple plant biological processes, − often occurs in CG, CHH, and CHG contexts in various regions of eukaryotic genomes. − Over the course of the whole developmental process during a plant life cycle, DNA methylation plays a key role in regulating multiple transitions, including the embryo to seedling, juvenile to adult, ,− and vegetative to reproductive , transitions. Previous studies have identified many DNA methylations and epigenetic changes associated with phase transitions in diverse plant species such as annual plants (e.g., Arabidopsis thaliana and rice) ,, and woody plants (e.g., apple, citrus, and grapevine). ,− …”

Section: Introductionmentioning

confidence: 99%

Epigenomic Regulatory Mechanism in Vegetative Phase Transition of Malus hupehensis

Xing

Zhou

et al. 2020

J. Agric. Food Chem.

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In woody plants, phase transitions substantially affect growth and development. Although there has been considerable interest in the regulatory mechanisms underlying phase changes, the associated epigenetic modifications remain relatively uncharacterized. We examined the DNA methylation changes and the transcriptional responses in adult and juvenile Malus hupehensis leaves. The DNA methylations were 66.61% and 68.3% in the CG context, 49.12% and 52.44% in the CHG context, and 7.02% and 8.22% in the CHH context for the adult and juvenile leaves, respectively. The number of differentially methylated regions in all contexts distributed in the genic regions varied. Additionally, inhibited DNA methylation in adult leaves activated the transcription of indole-3-acetic acid related genes in the signaling, response, and transport pathways. Moreover, the opposite methylation and expression patterns were observed for the SPL and AP2 family genes between the adult and juvenile leaves. Both gene families contribute to the M. hupehensis vegetative phase transition. Furthermore, the hyper-/hypomethylation of the gene body or promoter of transcription factor genes may lead to up-/downregulated gene expression. The methylation levels of the WRKY (22), NAC (21), ERF (8), WOX (2), KNAT (6), EIN3 (2), SCL (7), ZAT (7), and HSF (4) genes were higher in the adult leaves than in the juvenile leaves, whereas the opposite pattern was observed for the TCP (2), MADS-box (11), and DOF (3) genes. An analysis of the correlation between methylation and transcription indicated the methylation of the gene body in all contexts and the methylation of the promoter in the CG and CHG contexts are negatively correlated with gene expression. However, the methylation of the promoter in the CHH context is positively correlated with gene expression. These findings reflect the diversity in the epigenetic regulation of gene expression and may be useful for elucidating the epigenetic regulatory mechanism underlying the M. hupehensis vegetative phase transition.

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“…For instance, mutants affected in ATRX7 (H3K4 methyltransferase), EFS/SDG8 (H3K36 di-and trimethylation), EBS (an H3K4me2/3 "reader" interacting with HDA6) or HUB1 and HUB2 (H2B monoubiquitination) display lower ABI3 expression and dormancy, whereas those affected in H3K9 methylation (kyp/suvh4) or H3K4 demethylation (ldl1 and ldl2) display the opposite phenotype (Liu et al, 2007b;Bassel et al, 2011;Zheng et al, 2012;Zhao et al, 2015;Narro-Diego et al, 2017). Moreover, although PRC1/2 are not required for proper embryo development, mutations affecting PRC1 or PRC2 lead to a failure in both, the repression of LAFL expression and directly switch from embryo to seedling development (Chanvivattana et al, 2004;Makarevich et al, 2006;Aichinger et al, 2009;Bratzel et al, 2010;Chen et al, 2010;Berger et al, 2011;Bouyer et al, 2011;Muller et al, 2012;Tang et al, 2012a;Zhang et al, 2012;Deng et al, 2013;Yang et al, 2013;Molitor et al, 2014;Ikeuchi et al, 2015;Xiao and Wagner, 2015;Feng et al, 2016;Trindade et al, 2017;Xiao et al, 2017;Lee and Seo, 2018). Similar accumulation of seed proteins in vegetative tissues is also observed when the RETINOBLASTOMA-RELATED1 (RBR1) that is required to maintain the PRC2-dependent repression of LEC2 and ABI3 is affected (Gutzat et al, 2011;Kuwabara and Gruissem, 2014) and in mutant of the SWI2/SNF2 chromatin remodelling ATPase BRAHMA (BRM) (Tang et al, 2008), although BRM has been shown to controls the transition from juvenile to adult vegetative phase antagonistically to PRC2 (Xu et al, 2016).…”

Section: Chromatin-based Regulationsmentioning

confidence: 99%

Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development

et al. 2018

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The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.

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Epigenetic Regulation of Phase Transitions in Arabidopsis thaliana

Cited by 6 publications

References 157 publications

BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans

BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans

Epigenomic Regulatory Mechanism in Vegetative Phase Transition of Malus hupehensis

Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development

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