Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Nature ◽  
2011 ◽  
Vol 480 (7376) ◽  
pp. 245-249 ◽  
Author(s):  
Claude Becker ◽  
Jörg Hagmann ◽  
Jonas Müller ◽  
Daniel Koenig ◽  
Oliver Stegle ◽  
...  
2021 ◽  
Author(s):  
Vít Latzel ◽  
Javier Puy ◽  
Michael Thieme ◽  
Etienne Bucher ◽  
Lars Götzenberger ◽  
...  

AbstractAn accumulating body of evidence indicates that natural plant populations harbour a large diversity of transposable elements (TEs). TEs provide genetic and epigenetic variation that can substantially translate into changes in plant phenotypes. Despite the wealth of data on the ecological and evolutionary effects of TEs on plant individuals, we have virtually no information on the role of TEs on populations and ecosystem functioning. On the example of Arabidopsis thaliana, we demonstrate that TE-generated variation creates differentiation in ecologically important functional traits. In particular, we show that Arabidopsis populations with increasing diversity of individuals differing in copy numbers of the ONSEN retrotransposon had higher phenotypic and functional diversity. Moreover, increased diversity enhanced population productivity and reduced performance of interspecific competitors. We conclude that TE-generated diversity can have similar effects on ecosystem as usually documented for other biological diversity effects.


2016 ◽  
Vol 113 (14) ◽  
pp. E2083-E2092 ◽  
Author(s):  
Mélanie Rigal ◽  
Claude Becker ◽  
Thierry Pélissier ◽  
Romain Pogorelcnik ◽  
Jane Devos ◽  
...  

Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.


2018 ◽  
Vol 46 (6) ◽  
pp. 3019-3033 ◽  
Author(s):  
Lauriane Simon ◽  
Fernando A Rabanal ◽  
Tristan Dubos ◽  
Cecilia Oliver ◽  
Damien Lauber ◽  
...  

2017 ◽  
Author(s):  
Todd Blevins ◽  
Jing Wang ◽  
David Pflieger ◽  
Frédéric Pontvianne ◽  
Craig S. Pikaard

AbstractHybrid incompatibility resulting from deleterious gene combinations is thought to be an important step towards reproductive isolation and speciation. Here we demonstrate involvement of a silent epiallele in hybrid incompatibility. In Arabidopsis thaliana strain Col-0, one of the two copies of a duplicated histidine biosynthesis gene, HISN6B is not expressed, for reasons that have been unclear, making its paralog, HISN6A essential. By contrast, in strain Cvi-0, HISN6B is essential because HISN6A is mutated. As a result of these differences, Cvi-0 × Col-0 hybrid progeny that are homozygous for both Col-0 HISN6B and Cvi-0 HISN6A do not survive. We show that HISN6B is not a defective pseudogene in the Col-0 strain, but a stably silenced epiallele. Mutating HISTONE DEACETYLASE 6 (HDA6) or the cytosine methyltransferase genes, MET1 or CMT3 erases HISN6B’s silent locus identity in Col-0, reanimating the gene such that hisn6a lethality and hybrid incompatibility are circumvented. These results show that HISN6-dependent hybrid lethality is a revertible epigenetic phenomenon and provide additional evidence that epigenetic variation has the potential to limit gene flow between diverging populations of a species.Significance statementDeleterious mutations in different copies of a duplicated gene pair have the potential to cause hybrid incompatibility between diverging subpopulations, contributing to reproductive isolation and speciation. This study demonstrates a case of epigenetic gene silencing, rather than pseudogene creation by mutation, contributing to a lethal gene combination upon hybridization of two strains of Arabidopsis thaliana. The findings provide direct evidence that naturally occurring epigenetic variation can contribute to incompatible hybrid genotypes, reducing gene flow between strains of the same species.


1994 ◽  
Vol 5 (4) ◽  
pp. 551-558 ◽  
Author(s):  
Seok So Chang ◽  
Soon Ki Park ◽  
Byung Chul Kim ◽  
Bong Joong Kang ◽  
Dal Ung Kim ◽  
...  

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