ABSTRACT
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.
Subject(s)
Arabidopsis/genetics , Cell Nucleus/metabolism , DNA Methylation , DNA, Plant , Epigenesis, Genetic , Gene Expression Regulation, Plant , Genome, Plant , Genomic Instability , Arabidopsis/enzymology , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Base Composition , Cell Nucleus/enzymology , Chromatin Assembly and Disassembly , DNA (Cytosine-5-)-Methyltransferases/genetics , DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA, Ribosomal/metabolism , DNA-Binding Proteins/metabolism , Evolution, Molecular , Gene Expression Regulation, Developmental , Genotype , Heterochromatin/metabolism , Histones/metabolism , Methylation , Methyltransferases/metabolism , Mutation , Nuclear Proteins/metabolism , Phenotype , RNA Interference , RNA, Small Interfering/metabolism , Transcription Factors/metabolism , Transcription, GeneticABSTRACT
Constitutive heterochromatin is a compact, transcriptionally inert structure formed in gene-poor and repeat- and transposon-rich regions. In Arabidopsis, constitutive heterochromatin is characterized by hypermethylated DNA and histone H3 dimethylated at lysine (K) 9 (H3K9me2) together with depletion of histone H3 dimethylated at lysine 4 (H3K4me2). Here, we describe loci with intermediate properties of heterochromatin in which transcription downregulation is inherited in a manner similar to constitutive heterochromatin, although the loci are associated with opposing histone marks--H3K4me2 and H3K9me2. In the ddm1 (decrease in DNA methylation 1) mutants, their transcriptional activation is accompanied by the expected shift in the H3 modifications--depletion of H3K9me2 and enrichment in H3K4me2. In mom1 (Morpheus' molecule 1) mutants, however, a marked increase in transcription is not accompanied by detectable changes in the levels of H3K4me2 and H3K9me2. Therefore, transcriptional regulation in the intermediate heterochromatin involves two distinct epigenetic mechanisms. Interestingly, silent transgenic inserts seem to acquire properties characteristic of the intermediate heterochromatin.
