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

Maintenance of CG methylation ((m)CG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. However, functional links between (m)CG and other epigenetic mechanisms in vivo remain obscure. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining (m)CG, we find that (m)CG loss triggers genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms, which involve RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation, act in a stochastic and uncoordinated fashion. As a result, new and aberrant epigenetic patterns are progressively formed over several plant generations in the absence of (m)CG. Interestingly, the unconventional redistribution of epigenetic marks is necessary to "rescue" the loss of (m)CG, since mutant plants impaired in rescue activities are severely dwarfed and sterile. Our results provide evidence that (m)CG is a central coordinator of epigenetic memory that secures stable transgenerational inheritance in plants.

The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.