Extensive natural epigenetic variation at a [i]De Novo[/i] originated gene

Amanda Bortolini Silveira (1) , Charlotte Trontin (2) , Sandra Cortijo (3) , Joan Barau (1) , Luiz Eduardo Vieira del Bem (1) , Olivier Loudet (2) , Vincent Colot (3) , Michel Vincentz (4)

1 Center of Molecular Biology and Genetic Engineering
2 IJPB - Institut Jean-Pierre Bourgin
3 IBENS - Institut de biologie de l'ENS Paris
4 Center of Molecular Biology and Genetic Engineering - Department of Plant Biology

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 5'end 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 formation.

Domaines: Sciences du Vivant [q-bio]

Amanda Bortolini Silveira, Charlotte Trontin, Sandra Cortijo, Joan Barau, Luiz Eduardo Vieira del Bem, et al.. Extensive natural epigenetic variation at a [i]De Novo[/i] originated gene. PLoS Genetics, 2013, 9 (4), ⟨10.1371/journal.pgen.1003437⟩. ⟨hal-01190576⟩