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. The term ''epigenome'' refers to the genome-wide distribution of epigenetic marks such as DNA methylation, histone modifications, and the presence of histone variants (Jenuwein 2002). Specific combinations of these marks are thought to determine the local chromatin structure that affects transcription and genome stability (Jenuwein 2002). In plants and mammals, DNA methylation is the beststudied epigenetic modification. Its faithful propagation is not only critical for proper development but also silences transposable elements (Finnegan 1996;Miura et al. 2001;Singer et al. 2001;Kato et al. 2003;Chan et al. 2005). Thus, apart from a role in development, DNA methylation protects genome integrity.Methylation modifies cytosines preceding guanines ( m CG) and in plants METHYLTRANSFERASE 1 (MET1), a homolog of the mammalian Dnmt1, is required for propagating m CG patterns during DNA replication (Finnegan 1996). Loss of MET1 leads to almost a complete erasure of CG methylation and indirect losses of plantspecific non-CG methylation . Loss of MET1 also results in the suppression of DNA demethylation activities, altered RNA directed de novo methylation, and the redistribution of other repressive marks such as histone H3 dimethylation in Lys 9 and trimethylation in Lys 27 (Soppe et al. 2002;Tariq et al. 2003;Mathieu et al. 2005Mathieu et al. , 2007, creating further epigenetic variation. Thus, transgenerational inheritance of the epigenome in plants is coordinated by the faithful replication of m CG patterns (Mathieu et al. 2007). Notably, loss of m CG results in hypomethylated epi-alleles that, at some loci, may be stably inherited over many generations (Kakutani et al. 1996;Mathieu et al. 2007;Vaughn et al. 2007). This is similar to inheritance of epigenetic states of ribosomal DNA following intercrossed Arabidopsis accessions Richards 2002, 2005;Woo and Richards 2008

Transposable elements (TEs) contribute to genome size, organization and evolution. In plants, their activity is primarily controlled by transcriptional gene silencing (TGS), usually investigated at steady states, reflecting how long-established silent conditions are maintained, faithfully reiterated or temporarily modified. How active, invasive TEs are detected and silenced de novo in plants remains largely unknown. Using inbred lineages of hybrid Arabidopsis thaliana epigenomes combining wild-type and mutant chromosomes, we have deciphered the sequence of physiological and molecular events underlying the de novo invasion, proliferation and eventual demise of the single-copy endogenous retrotransposon Evadé (EVD). We show how this reconstructed TE burst causes widespread genome diversification and de novo epiallelism that could serve as sources for selectable and potentially adaptive traits.

Retroelements, the prevalent class of plant transposons, have major impacts on host genome integrity and evolution. They produce multiple proteins from highly compact genomes and, similar to viruses, must have evolved original strategies to optimize gene expression, although this aspect has been seldom investigated thus far. Here, we have established a high-resolution transcriptome/translatome map for the near-entirety of transposons, using two distinct DNA methylation mutants in which transposon expression is broadly de-repressed. The value of this map to study potentially intact and transcriptionally active transposons in is illustrated by our comprehensive analysis of the cotranscriptional and translational features of elements, a family of young and active retroelements in plant genomes, and how such features impact their biology. Genome-wide transcript profiling revealed a unique and widely conserved alternative splicing event coupled to premature termination that allows for the synthesis of a short subgenomic RNA solely dedicated to production of the GAG structural protein and that preferentially associates with polysomes for efficient translation. Mutations engineered in a transgenic version of the element further show how alternative splicing is crucial for the appropriate coordination of full-length and subgenomic RNA transcription. We propose that this hitherto undescribed genome expression strategy, conserved among plant elements, enables an excess of structural versus catalytic components, mandatory for mobilization.