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Extensive Natural Epigenetic Variation at a De Novo Originated Gene

Amanda Bortolini Silveira, Charlotte Trontin, Sandra Cortijo, Joan Barau, Luiz Eduardo Vieira Del Bem, Olivier Loudet, Vincent Colot, Michel Vincentz

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 thaliana, which is involved in starch metabolism and that originated de
novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies
considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate
that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 59end of
the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for
several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first
indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of