Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN) sites within the body of a non-repetitive tomato gene

González, Rodrigo M.; Ricardi, Martiniano M.; Iusem, Norberto D.
January 2011
BMC Plant Biology;2011, Vol. 11 Issue 1, p94
Academic Journal
Background: Eukaryotic DNA methylation is one of the most studied epigenetic processes, as it results in a direct and heritable covalent modification triggered by external stimuli. In contrast to mammals, plant DNA methylation, which is stimulated by external cues exemplified by various abiotic types of stress, is often found not only at CG sites but also at CNG (N denoting A, C or T) and CNN (asymmetric) sites. A genome-wide analysis of DNA methylation in Arabidopsis has shown that CNN methylation is preferentially concentrated in transposon genes and non-coding repetitive elements. We are particularly interested in investigating the epigenetics of plant species with larger and more complex genomes than Arabidopsis, particularly with regards to the associated alterations elicited by abiotic stress. Results: We describe the existence of CNN-methylated epialleles that span Asr1, a non-transposon, protein-coding gene from tomato plants that lacks an orthologous counterpart in Arabidopsis. In addition, to test the hypothesis of a link between epigenetics modifications and the adaptation of crop plants to abiotic stress, we exhaustively explored the cytosine methylation status in leaf Asr1 DNA, a model gene in our system, resulting from water-deficit stress conditions imposed on tomato plants. We found that drought conditions brought about removal of methyl marks at approximately 75 of the 110 asymmetric (CNN) sites analysed, concomitantly with a decrease of the repressive H3K27me3 epigenetic mark and a large induction of expression at the RNA level. When pinpointing those sites, we observed that demethylation occurred mostly in the intronic region. Conclusions: These results demonstrate a novel genomic distribution of CNN methylation, namely in the transcribed region of a protein-coding, non-repetitive gene, and the changes in those epigenetic marks that are caused by water stress. These findings may represent a general mechanism for the acquisition of new epialleles in somatic cells, which are pivotal for regulating gene expression in plants.


Related Articles

  • RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids. Meng Chen; Ha, Misook; Lackey, Erika; Jianlin Wang; Chen, Z. Jeffrey // Genetics;Apr2008, Vol. 178 Issue 4, p1845 

    Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecicais a natural...

  • Gardening the genome: DNA methylation in Arabidopsis thaliana. Chan, Simon W. -L.; Henderson, Ian R.; Jacobsen, Steven E. // Nature Reviews Genetics;May2005, Vol. 6 Issue 5, p351 

    DNA methylation has two essential roles in plants and animals-defending the genome against transposons and regulating gene expression. Recent experiments in Arabidopsis thaliana have begun to address crucial questions about how DNA methylation is established and maintained. One cardinal insight...

  • DNA demethylation: a lesson from the garden. Ikeda, Yoko; Kinoshita, Tetsu // Chromosoma;Feb2009, Vol. 118 Issue 1, p37 

    Gene silencing by DNA methylation is well documented and known to be essential for various biological phenomena in many organisms. In contrast, the processes that convert the silent state of a gene whose DNA is methylated and predicted to form facultative heterochromatin to the actively...

  • The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression. Bilichak, Andriy; Ilnystkyy, Yaroslav; Hollunder, Jens; Kovalchuk, Igor // PLoS ONE;Jan2012, Vol. 7 Issue 1, p1 

    Plants are able to acclimate to new growth conditions on a relatively short time-scale. Recently, we showed that the progeny of plants exposed to various abiotic stresses exhibited changes in genome stability, methylation patterns and stress tolerance. Here, we performed a more detailed analysis...

  • Nucleolin Is Required for DNA Methylation State and the Expression of rRNA Gene Variants in Arabidopsis thaliana.  // PLoS Genetics;Nov2010, Vol. 6 Issue 11, p1 

    No abstract available.

  • Tuning in to flower power. Pflumm, Michelle // Nature Methods;Jun2008, Vol. 5 Issue 6, p463 

    The article focuses on the research which illustrates how DNA methylation is regulated in Arabidopsis thaliana. DNA methylation is used to improve gene expression and to remove transposon invaders. Researchers first used immunoprecipitation and hybridization to identify methylated sequences but...

  • A silent pas de deux. Amoils, Shannon // Nature Reviews Molecular Cell Biology;Feb2007, Vol. 8 Issue 2, p94 

    The article discusses a study on DNA methylation and transcription. The study by Steven Henikoff and colleagues on Arabidopsis thaliana plant reveal that DNA methylation and transcription are closely linked and interdependent. The study also reveals that methylation is more likely in moderately...

  • Generation of a luciferase-based reporter for CHH and CG DNA methylation in Arabidopsis thaliana. Dinh, Thanh Theresa; O'Leary, Michael; So Youn Won; Shengben Li; Arroyo, Lorena; Xigang Liu; Defries, Andrew; Binglian Zheng; Cutler, Sean R.; Xuemei Chen // Silence;2013, Vol. 4 Issue 1, p1 

    Background: DNA methylation ensures genome integrity and regulates gene expression in diverse eukaryotes. In Arabidopsis, methylation occurs in three sequence contexts: CG, CHG and CHH. The initial establishment of DNA methylation at all three sequence contexts occurs through a process known as...

  • Extensive Natural Epigenetic Variation at a De Novo Originated Gene. Silveira, Amanda Bortolini; Trontin, Charlotte; Cortijo, Sandra; Barau, Joan; Bem, Luiz Eduardo Vieira Del; Loudet, Olivier; Colot, Vincent; Vincentz, Michel // PLoS Genetics;Apr2013, Vol. 9 Issue 4, Special section p1 

    Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics