Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes

Jon Reinders; Brande B.H. Wulff; Marie Mirouze; Arturo Marí-Ordóñez; Mélanie Dapp; Wilfried Rozhon; Etienne Bucher; Grégory Theiler; Jerzy Paszkowski

doi:10.1101/gad.524609

Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes

¹Department of Plant Biology, University of Geneva, Sciences III, CH-1211 Geneva 4, Switzerland;
²Instituto de Biología Molecular y Celular de Plantas (IBMCP), UPV-CSIC, 46022 Valencia, Spain;
³Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria

Abstract

Transgenerational epigenetic inheritance has been defined by the study of relatively few loci. We examined a population of recombinant inbred lines with epigenetically mosaic chromosomes consisting of wild-type and CG methylation-depleted segments (epiRILs). Surprisingly, transposons that were immobile in the parental lines displayed stochastic movement in 28% of the epiRILs. Although analysis after eight generations of inbreeding, supported by genome-wide DNA methylation profiling, identified recombined parental chromosomal segments, these were interspersed with unexpectedly high frequencies of nonparental methylation polymorphism. Hence, epigenetic inheritance in hybrids derived from parents with divergent epigenomes permits long-lasting epi-allelic interactions that violate Mendelian expectations. Such persistently “unstable” epigenetic states complicate linkage-based epigenomic mapping. Thus, future epigenomic analyses should consider possible genetic instabilities and alternative mapping strategies.

Keywords

Footnotes

↵4 Present address: Institut de Biologie Moléculaire des Plantes, CNRS UPR 2353, Université Louis Pasteur, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France.
↵5 Corresponding authors.

↵E-MAIL jerzy.paszkowski{at}unige.ch; FAX 41-22-379-3107.
↵6 E-MAIL jon.reinders{at}unige.ch; FAX 41-22-379-3107.
Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.524609.
Supplemental material is available at http://www.genesdev.org.
- Received January 29, 2009.
- Accepted March 13, 2009.