<scp>DNA</scp>
            sequence properties that predict susceptibility to epiallelic switching

Catoni, Marco; Griffiths, J.; Becker, Claude; Zabet, Nicolae Radu; Bayón, Carlos; Dapp, Mélanie; Lieberman‐Lazarovich, Michal; Weigel, Detlef; Paszkowski, Jerzy

doi:10.15252/embj.201695602

Cited by 61 publications

(78 citation statements)

References 35 publications

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“…All six lines selected from top performing F 2 plants showed a reduction of enhanced growth by F 2:6 , further confirming the epigenetic nature of MSH1-derived growth changes, with similar dissipation patterns described previously in Arabidopsis ddm1 epiRILs (Cortijo et al, 2014;Roux et al, 2011). A recent study has suggested that stability and switching of acquired epigenetic states are influenced by DNA sequence composition and repetitiveness (Catoni et al, 2017). It is also speculated that methylation variation not linked to a causal genetic variant tends to be less stable than when directly linked to genetic change (Schmitz et al, 2013).…”

Section: Discussionsupporting

confidence: 87%

An epigenetic breeding system in soybean for increased yield and stability

Raju

Shao

Sanchez

et al. 2017

Preprint

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Epigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant-specific gene, MutS HOMOLOG1 (MSH1), in multiple plant species produces a range of developmental changes accompanied by modulation of defense, phytohormone, and abiotic stress response pathways. This msh1-conditioned developmental reprogramming is retained independent of transgene segregation, giving rise to transgene-null 'memory' effects. An isogenic memory line crossed to wild type produces progeny families displaying increased variation in adaptive traits that respond to selection. This study investigates amenability of the MSH1 system for inducing epigenetic variation in soybean that may be of value agronomically. We developed epi-line populations by crossing with msh1-acquired soybean memory lines. Derived soybean epi-lines showed increase in variance for multiple yield-related traits including pods per plant, seed weight, and maturity time in both greenhouse and field trials. Selected epi-F 2:4 and epi-F 2:5 lines showed an increase in seed yield over wild type. By epi-F 2:6, we observed a return of MSH1-derived enhanced growth back to wild type levels. Epi-populations also showed evidence of reduced epitype-by-environment (e x E) interaction, indicating higher yield stability. Transcript profiling of the soybean epi-lines identified putative signatures of enhanced growth behavior across generations. Genes related to cell cycle, abscisic acid biosynthesis, and auxinresponse, particularly SMALL AUXIN UP RNAs (SAURs), were differentially expressed in epi-F 2:4 lines that showed increased yield when compared to epi-F 2:6 . These data support the potential of MSH1-derived epigenetic variation in plant breeding for enhanced yield and yield stability.

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Section: Discussionsupporting

confidence: 87%

An epigenetic breeding system in soybean for increased yield and stability

Raju

Shao

Sanchez

et al. 2017

Preprint

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“…They found that proximal methylation levels are most predictive. In a slightly different setting, Catoni et al (2017) identified features in transposable element-like sequence, including high repeat content and low CG density, that predict the efficient re-establishment of CG methylation loss in lines following transient disruption of an enzyme responsible for maintenance of CG methylation. Following in these footsteps, comprehensive deep learning approaches are underway to identify chromatin and sequence features that determine the 'epimutability' of specific loci in plant genomes.…”

Section: Predicting the 'Epimutability' Of Specific Locimentioning

confidence: 99%

Spontaneous epimutations in plants

2018

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Contents Summary I. Introduction II. What is the rate and molecular spectrum of spontaneous epimutations? III. Do spontaneous epimutations have phenotypic consequences? IV. Conclusion and discussion Acknowledgements References SUMMARY: Heritable gains or losses of cytosine methylation can arise stochastically in plant genomes independently of DNA sequence changes. These so-called 'spontaneous epimutations' appear to be a byproduct of imperfect DNA methylation maintenance and epigenome reinforcement events that occur in specialized cell types. There is continued interest in the plant epigenetics community in trying to understand the broader implications of these stochastic events, as some have been shown to induce heritable gene expression changes, shape patterns of methylation diversity within and among plant populations, and appear to be responsive to multi-generational environmental stressors. In this paper we synthesized our current knowledge of the molecular basis and functional consequences of spontaneous epimutations in plants, discuss technical and conceptual challenges, and highlight emerging research directions.

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“…Converted samples were immediately used to prepare bisulfite libraries employing the TrueSeq DNA 259 We computed chloroplast mappability on the eggplant genome using the gem-mappability tool from the Gem 275 library (Derrien et al, 2012), with a k-mer size of 75 bp and allowing a maximum of one mismatch, and only 276 unique regions (mappability = 1) were used to estimate conversion. To account for non-converted DNA, we 277 applied a correction according to Catoni et al (2017). Briefly, the number of methylated reads were decreased 278 as: m*= max(0, mnc) (where m* is the corrected number of methylated reads, m is the raw number of 279 methylated reads, n is the total number of reads and c is the conversion rate).…”

Section: Library Preparation and Sequencing 258mentioning

confidence: 99%

Epigenetic bases of grafting-induced vigour in eggplant

Cerruti

Gisbert

Drost

et al. 2019

Preprint

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27In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This 28 is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Despite its 29 wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain 30 largely unknown. Given that epigenetics plays a crucial role during distance signalling in plants, we studied 31 the genome-wide changes induced by DNA methylation in eggplant (Solanum melongena) plants grafted onto 32 two interspecific rootstocks used to increase scion vigour. As a control, we compared any epigenetic effect 33 found in such grafts to patterns detected in self-grafted plants. We found that vigour was associated with a 34 specific change in scion gene expression and a genome-wide hypomethylation in CHH context. Interestingly, 35 this hypomethylation correlated with the down-regulation of younger and potentially more active LTR 36 retrotransposons (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated to both 37 physiological and molecular phenotypes in grafted plants. We propose that rootstocks can promote vigour by 38 reducing DNA methylation in the scion genome, following similar principles found in some heterotic hybrids. 39 40

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DNA sequence properties that predict susceptibility to epiallelic switching

Cited by 61 publications

References 35 publications

An epigenetic breeding system in soybean for increased yield and stability

An epigenetic breeding system in soybean for increased yield and stability

Spontaneous epimutations in plants

Epigenetic bases of grafting-induced vigour in eggplant

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