1. Department of Plant Biology, University of Geneva, Sciences III, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
2. Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
3. Centre National de la Recherche Scientifique (CNRS), UMR 6247, GReD, INSERM U 931, 24 avenue des Landais, Clermont Université, 63177 Aubière, France
4. These authors contributed equally to this work.

Correspondence to: Jerzy Paszkowski¹Olivier Mathieu^1,3 Correspondence and requests for materials should be addressed to J.P. (Email: jerzy.paszkowski@unige.ch) or O.M. (Email: olivier.mathieu@univ-bpclermont.fr).

Abstract

Retrotransposons are mobile genetic elements that populate chromosomes, where the host largely controls their activities^{1, 2, 3}. In plants and mammals, retrotransposons are transcriptionally silenced by DNA methylation^{1, 4}, which in Arabidopsis is propagated at CG dinucleotides by METHYLTRANSFERASE 1 (MET1)⁵. In met1 mutants, however, mobilization of retrotransposons is not observed, despite their transcriptional activation^{4, 5, 6}. A post-transcriptional mechanism therefore seems to be preventing retrotransposition. Here we show that a copia-type retrotransposon (Évadé, French for 'fugitive') evaded suppression of its movement during inbreeding of hybrid epigenomes consisting of met1- and wild-type-derived chromosomes. Évadé (EVD) reinsertions caused a series of developmental mutations that allowed its identification. Genetic testing of host control of the EVD life cycle showed that transcriptional suppression occurred by CG methylation supported by RNA-directed DNA methylation. On transcriptional reactivation, subsequent steps of the EVD cycle were inhibited by plant-specific RNA polymerase IV/V^{7, 8} and the histone methyltransferase KRYPTONITE (KYP). Moreover, genome resequencing demonstrated retrotransposition of EVD but no other potentially active retroelements when this combination of epigenetic mechanisms was compromised. Our results demonstrate that epigenetic control of retrotransposons extends beyond transcriptional suppression and can be individualized for particular elements.