EpiRILs

Catoni, Marco; Cortijo, Sandra

doi:10.1016/bs.abr.2018.08.002

Cited by 9 publications

(5 citation statements)

References 113 publications

(108 reference statements)

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“…Hence, LTR-TEs can be a valuable tool in plant breeding but only if their activity is under strict control. So far, the application of DNA methyltransferase inhibitors has been efficiently used to induce epigenetic changes and activate LTR-TEs in plants ( Griffin et al, 2016 ; Thieme et al, 2017 ; Catoni and Cortijo, 2018 ; Roquis et al, 2021 ). In contrast to these chemicals, Tenofovir is a drug with a specific inhibitory effect on LTR-TE mobilization, acting with a mechanism which is independent on the alteration of RNA silencing or associated epigenetic mechanisms.…”

Section: Discussionmentioning

confidence: 99%

“…This leads to phenotypic abnormalities and transgenerational decrease of fitness ( Mirouze et al, 2009 ; Tsukahara et al, 2009 ; Griffiths et al, 2018 ). Interestingly, these effects remain mostly evident in crosses of MET1 and DDM1 mutants with isogenic wild-type lines, and in their segregating wild-type progenies ( Catoni and Cortijo, 2018 ). Specifically, several TEs were found to remain mobile for up to eight generations following the re-establishment of wild-type alleles in epigenetic recombinant inbred lines obtained from one met1 or ddm1 original parent ( Catoni et al, 2019 ; Quadrana et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

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Specific suppression of long terminal repeat retrotransposon mobilization in plants

et al. 2022

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The tissue culture passage necessary for generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilisation of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here we demonstrate that in conditions inductive for high LTR-TE mobilisation, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the Reverse Transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of Oryza sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Specific suppression of long terminal repeat retrotransposon mobilization in plants

et al. 2022

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“…Furthermore, to investigate if the asymmetric change in C.V. observed in met1-1 was masked in met1-3 background due to the high number of genes that change expression, we took advantage of epigenetic recombinant inbred lines (epiRILs) generated by a cross between Col-0 and met1-3 plants, and propagated by single seed descend (Catoni & Cortijo;Reinders et al, 2009). Each epiRIL line plant displays parts of the genome inherited from a Col-0 epigenetic state and parts from the genome in met1-3 epigenetic state, but they all contain a wild type allele of MET1 gene.…”

Section: Gene Expression Variability In Epigenetic Recombinant Inbred...mentioning

confidence: 99%

Gene body methylation buffers noise in gene expression in plants

Zastąpiło,

Emmerson,

Mikheeva

et al. 2024

Preprint

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Non-genetic variability in gene expression is an inevitable consequence of stochastic nature of processes driving transcription and translation. Largely thought to be deleterious to cell fitness, it is not uniform across the transcriptome. This implies the existence of (molecular) determinants affecting the degree of gene expression variability, although this remain poorly understood in multicellular systems. In this study, we found a link between gene body methylation and noise in gene expression inArabidopsis thaliana. More specifically, genes with high levels of noise show low levels of gene body methylation, while genes with lower level of noise in gene expression show higher level of gene body methylation. Most importantly, loss of CpG methylation in gene bodies lead to a significant number of genes displaying higher noise in gene expression. This could be compensated by low but significant gain of non-CpG methylation at promoters of certain genes. Overall, our results show that gene body methylation has a functional role and specifically controls the noise in gene expression for a large number of genes.

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“…These epigenetic changes play a role in the regulation of chromatin structure and control the accessibility of DNA ( Robertson, 2005 ; Lang et al., 2017 ). Epigenetic variation can generate epigenetic alleles (or epialleles) with different degrees of stability, which are transmitted during DNA replication and often mitotically passed to progeny in a Mendelian fashion ( Weigel and Colot, 2012 ; Catoni and Cortijo, 2018 ). In the previous chapter, we discussed how mobile RNA molecules travelling across the graft junction can trigger epigenetic changes at specific target loci in recipient tissues.…”

Section: Changes To the Epigenome Associate To Graftingmentioning

confidence: 99%

Long distance signalling and epigenetic changes in crop grafting

Jeynes-Cupper

Catoni

2023

Front. Plant Sci.

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Humans have used grafting for more than 4000 years to improve plant production, through physically joining two different plants, which can continue to grow as a single organism. Today, grafting is becoming increasingly more popular as a technique to increase the production of herbaceous horticultural crops, where rootstocks can introduce traits such as resistance to several pathogens and/or improving the plant vigour. Research in model plants have documented how long-distance signalling mechanisms across the graft junction, together with epigenetic regulation, can produce molecular and phenotypic changes in grafted plants. Yet, most of the studied examples rely on proof-of-concept experiments or on limited specific cases. This review explores the link between research findings in model plants and crop species. We analyse studies investigating the movement of signalling molecules across the graft junction and their implications on epigenetic regulation. The improvement of genomics analyses and the increased availability of genetic resources has allowed to collect more information on potential benefits of grafting in horticultural crop models. Ultimately, further research into this topic will enhance our ability to use the grafting technique to exploit genetic and epigenetic variation in crops, as an alternative to traditional breeding.

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EpiRILs

Cited by 9 publications

References 113 publications

Specific suppression of long terminal repeat retrotransposon mobilization in plants

Specific suppression of long terminal repeat retrotransposon mobilization in plants

Gene body methylation buffers noise in gene expression in plants

Long distance signalling and epigenetic changes in crop grafting

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