Epigenetic Natural Variation in Arabidopsis thaliana

Vaughn, Matthew; Tanurdžić, Miloš; Lippman, Zachary B.; Jiang, Hongmei; Carrasquillo, Robert; Rabinowicz, Pablo D.; Dedhia, Neilay; McCombie, W. Richard; Agier, Nicolas; Bulski, Agnès; Colot, Vincent; Doerge, R. W.; Martienssen, Robert A.

doi:10.1371/journal.pbio.0050174

Cited by 398 publications

(399 citation statements)

References 62 publications

(149 reference statements)

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Section: Sequence Context and Genomic Distribution Of Dna Methylationmentioning

confidence: 93%

“…As mentioned earlier, DNA methylation of repeat elements is mostly constant among Arabidopsis accessions (Vaughn et al, 2007;Zhai et al, 2008;Zhang et al, 2008), yet some highly methylated repeat elements seem to produce hardly any siRNAs (Kasschau et al, 2007;Lister et al, 2008;Teixeira et al, 2009). This raises the question of how such repeat elements maintain DNA methylation over evolutionary time.…”

Section: Transgenerational Inheritance Of Dna Methylation Patternsmentioning

confidence: 95%

“…In addition, the two whole-genome bisulfite sequencing studies cited above established that gene body methylation is restricted almost exclusively to CG sites (Cokus et al, 2008;Lister et al, 2008). Furthermore, genes appear to display variable DNA methylation between Arabidopsis accessions (Vaughn et al, 2007;Zhang et al, 2008). Although current evidence suggests that gene body methylation is a by-product of transcription by RNA Polymerase II (Pol II) and has limited functional consequences Law and Jacobsen, 2010), the extent to which it varies in relation to transcriptional activity during development, or in response to environmental changes, remains to be determined.…”

Section: Sequence Context and Genomic Distribution Of Dna Methylationmentioning

confidence: 99%

“…Furthermore, this dense DNA methylation strongly correlates with dimethylation of histone H3 lysine 9 (H3K9me2), a classic heterochromatic mark, and transcriptional silencing . Finally, DNA methylation of repeat elements is consistent across Arabidopsis accessions (Vaughn et al, 2007;Zhang et al, 2008), indicating that it is stably deposited over these sequences and/or that its absence is strongly counter selected.Early genome-wide mapping of DNA methylation in Arabidopsis using tiling arrays revealed that, in addition to repeat elements, 20-30% of Arabidopsis genes are methylated Zilberman et al, 2007). This gene methylation is restricted to only part of the transcribed region and is associated with expression rather than silencing (Zilberman et al, 2007).…”

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Repeat elements and the Arabidopsis DNA methylation landscape

Teixeira

Colot

2010

Heredity

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DNA methylation is an epigenetic mark that has key roles in the control of genome activity in plants and mammals. It is critical for the stable silencing of repeat elements and is also involved in the epigenetic regulation of some genes. Despite similarities in the controlling functions of DNA methylation, its dynamics and deposition patterns differ in several respects between plants and mammals. One of the most striking differences is that plants tend to propagate pre-existing DNA methylation states across generations, whereas mammals re-establish them genome wide at every generation. Here, we review our current understanding of DNA methylation in the flowering plant Arabidopsis. We discuss in particular the role of RNAi in the incremental methylation and silencing of repeat elements over successive generations. We argue that paramutation, an epigenetic phenomenon first described in maize, is an extreme manifestation of this RNAi-dependent pathway. Heredity (2010) 105, 14-23; doi:10.1038/hdy.2010.52; published online 12 May 2010Keywords: DNA methylation; repeat elements; Arabidopsis; RNAi; paramutation Introduction DNA methylation refers to the enzymatic transfer of a methyl group to specific nucleotides within the DNA sequence. In eukaryotes, this modification almost exclusively affects cytosines. Although clearly ancestral, cytosine methylation is not universally present in the eukaryotic tree of life. Thus, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, as well as the nematode Caenorhabditis elegans have no DNA methyltransferases (DNA MTases;Goll and Bestor, 2005). Furthermore, Drosophila contains a single, enigmatic DNA MTase-like protein (Goll and Bestor, 2005) and it is unclear if this species actually methylates DNA. By contrast, DNA methylation is readily detected in plants and mammals, where it is critical for normal development and genome stability. Although numerous hypotheses have been proposed (Bird, 1995;Yoder et al., 1997;Martienssen, 1998;Regev et al., 1998;Colot and Rossignol, 1999;Suzuki and Bird, 2008), it is still a mystery as to why these organisms cannot dispense with cytosine methylation when many lower eukaryotes can.In plants and mammals, most methylated cytosines are found over repeat elements (Goll and Bestor, 2005;Suzuki and Bird, 2008;Law and Jacobsen, 2010) and loss of this modification is associated with transcriptional reactivation as well as increased mobilization of transposable elements (TEs; Slotkin and Martienssen, 2007). These observations likely reflect the ancestral role of cytosine methylation in the defence against invasive DNA. Methylation of repeat elements is also thought to have been exapted recurrently during eukaryotic evolution to exert other essential functions, notably in the epigenetic regulation of genes. Thus, genomic imprinting, which results in parent-of-origin-dependent expression, may have evolved in plants and mammals from situations in which methylation of repeat elements influences the activity of neighbouring genes (Barlow, 1993;M...

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Section: Sequence Context and Genomic Distribution Of Dna Methylationmentioning

confidence: 93%

Section: Transgenerational Inheritance Of Dna Methylation Patternsmentioning

confidence: 95%

Section: Sequence Context and Genomic Distribution Of Dna Methylationmentioning

confidence: 99%

mentioning

confidence: 93%

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Repeat elements and the Arabidopsis DNA methylation landscape

Teixeira

Colot

2010

Heredity

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“…Ecotypes of Arabidopsis collected from drastically differing environments have also been compared in several epigenomic studies. As well as DNA methylation differences (Vaughn et al, 2007), ecotypes differ in their short interfering RNA complements (Zhai et al, 2008).…”

Section: Measuring Epigenetic Variation In Populationsmentioning

confidence: 99%

Epigenomic plasticity within populations: its evolutionary significance and potential

Johnson

Tricker

2010

Heredity

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Epigenetics has progressed rapidly from an obscure quirk of heredity into a data-heavy 'omic' science. Our understanding of the molecular mechanisms of epigenomic regulation, and the extent of its importance in nature, are far from complete, but in spite of such drawbacks, population-level studies are extremely valuable: epigenomic regulation is involved in several processes central to evolutionary biology including phenotypic plasticity, evolvability and the mediation of intragenomic conflicts. The first studies of epigenomic variation within populations suggest high levels of phenotypically relevant variation, with the patterns of epigenetic regulation varying between individuals and genome regions as well as with environment. Epigenetic mechanisms appear to function primarily as genome defences, but result in the maintenance of plasticity together with a degree of buffering of developmental programmes; periodic breakdown of epigenetic buffering could potentially cause variation in rates of phenotypic evolution.

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Epigenetic inheritance and plant evolution

Miryeganeh

Saze

2019

Population Ecology

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Being sessile organisms, plants show a high degree of developmental plasticity to cope with a constantly changing environment. While plasticity in plants is largely controlled genetically, recent studies have demonstrated the importance of epigenetic mechanisms, especially DNA methylation, for gene regulation and phenotypic plasticity in response to internal and external stimuli. Induced epigenetic changes can be a source of phenotypic variations in natural plant populations that can be inherited by progeny for multiple generations. Whether epigenetic phenotypic changes are advantageous in a given environment, and whether they are subject to natural selection is of great interest, and their roles in adaptation and evolution are an area of active research in plant ecology. This review is focused on the role of heritable epigenetic variation induced by environmental changes, and its potential influence on adaptation and evolution in plants.

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Epigenetic Natural Variation in Arabidopsis thaliana

Cited by 398 publications

References 62 publications

Repeat elements and the Arabidopsis DNA methylation landscape

Repeat elements and the Arabidopsis DNA methylation landscape

Epigenomic plasticity within populations: its evolutionary significance and potential

Epigenetic inheritance and plant evolution

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