RESEARCH HIGHLIGHTS Nature Reviews Genetics | AOP, published online 29 July 2014; doi:10.1038/nrg3797

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Switching phenotypes with epialleles

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Epiallelic variation could underlie important phenotypic differences among natural plant populations. Two studies now provide evidence for such an effect in secondary metabolism and reproduction. Quadrana et al. sought to better understand the factors underlying vitamin E content heritability in cultivated tomato plants by focusing on a previously detected vitamin E quantitative trait locus (QTL). They used a combination of reverse genetic approaches, expression analyses, DNA methylation assays and small interfering RNA (siRNA) profiling to show that methyl­ation QTL9-2-6 is associated with differential methylation of a transposable element (TE) in the promoter of VTE3 (which encodes a protein involved in the biosynthesis

of vitamin E). This DNA methylation can be spontaneously reverted, which directly increases VTE3 expression and vitamin E content in tomatoes. These data show that naturally occurring epialleles are linked with the regulation of a nutritionally important element and demonstrate the importance of epigenetics in determining such traits. In the second study, Pignatta et al. examined variations in imprinting (which arises from the differential DNA methylation of parental alleles) and epigenetic polymorphisms in Arabidopsis thaliana. The researchers looked at genome-wide DNA methyl­ation patterns, as well as small RNA and gene expression patterns in the seeds, embryo and endosperm (that is, the tissue inside the seeds of

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flowering plants where imprinting primarily occurs) of various strains. They found 12 examples of allelespecific imprinting, approximately half of which were associated with endosperm demethyl­ation of a TE. Further analysis on a larger data set enabled the researchers to predict imprinting status on the basis of epigenetic differences at TEs. Naturally occurring epialleles can have a substantial phenotypic effect when patterns of methylation are altered. Importantly, these findings show that the apparently low heritability of some traits might now be re-interpreted, as the instability of some epigenetic and reversible methylation QTLs can result in dynamic traits with heritability that cannot be predicted from traditional Mendelian models.

Bryony Jones

ORIGINAL RESEARCH PAPERS Quadrana, L. et al. Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nature Commun. 5, 4027 (2014) | Pignatta, D. et al. Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. Elife http://dx.doi. org/10.7554/eLife.03198 (2014)

VOLUME 15 | SEPTEMBER 2014 © 2014 Macmillan Publishers Limited. All rights reserved

DNA methylation: Switching phenotypes with epialleles.

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