Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation

A histone H3 methyltransferase controls DNA methylation in Neurospora crassa

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. We have demonstrated previously that dim-2 encodes a DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora crassa. Here we report that another Neurospora gene, dim-5, is required for DNA methylation, as well as for normal growth and full fertility. We mapped dim-5 and identified it by transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a gene related to histone methyltransferases that are involved in heterochromatin formation in other organisms. Transformation of a wild-type strain with a segment of dim-5 reactivated a silenced hph gene, apparently by 'quelling' of dim-5. We demonstrate that recombinant DIM-5 protein specifically methylates histone H3 and that replacement of lysine 9 in histone H3 with either a leucine or an arginine phenocopies the dim-5 mutation. We conclude that DNA methylation depends on histone methylation.

Silencing of transposable elements in plants

Plant genomes contain many transposable elements, most of which are inactivated or 'silenced'. Recent studies have brought significant new insights into the regulation of transposable elements. In Caenorhabditis elegans, they are silenced post-transcriptionally, whereas transposable elements in Arabidopsis are silenced by a chromatin-remodelling factor, one of the components of transcriptional gene silencing. These observations provide the functional correlation between gene silencing and the suppression of transposable elements, and have major implications for our understanding of the maintenance of genomic integrity.

Chromatin remodelling

Epigenetic mechanisms are heritable traits that are mediated by changes in a genetic locus that do not involve a modification at the nucleotide level. As eukaryotic DNA is organised in chromatin units, epigenetic modifications can be mediated by chromatin remodelling. Although there are a number of well-characterised chromatin remodelling factors to which we can allocate a defined molecular function, we need to understand chromatin remodelling processes as the combined effects of such factors in higher order complexes.

Molecular biology of the chromo domain: an ancient chromatin module comes of age

The chromo domain motif is found in proteins from fungi, protists, plants, fish, insects, amphibians, birds, and mammals. The chromo domain peptide fold may have its origins as a chromosomal protein in a common ancestor of archea and eukaryota, making it a particularly ancient protein structural module. Chromo domains have been found in single or multiple copies in proteins with diverse structures and activities, most or all of which are connected with chromosome structure/function. In this review, our current knowledge of chromo domain properties is summarized and a variety of contexts in which chromo domains participate in aspects of chromatin metabolism are discussed.

DNA methylation and epigenetic inheritance in plants and filamentous fungi

Plants and filamentous fungi share with mammals enzymes responsible for DNA methylation. In these organisms, DNA methylation is associated with gene silencing and transposon control. However, plants and fungi differ from mammals in the genomic distribution, sequence specificity, and heritability of methylation. We consider the role that transposons play in establishing methylation patterns and the epigenetic consequences of their perturbation.

RNA: guiding gene silencing

In diverse organisms, small RNAs derived from cleavage of double-stranded RNA can trigger epigenetic gene silencing in the cytoplasm and at the genome level. Small RNAs can guide posttranscriptional degradation of complementary messenger RNAs and, in plants, transcriptional gene silencing by methylation of homologous DNA sequences. RNA silencing is a potent means to counteract foreign sequences and could play an important role in plant and animal development.

Translating the histone code

Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a "histone code" that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.

Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene

Plants maintain cytosine methylation at CG and non-CG residues to control gene expression and genome stability. In a screen for Arabidopsis mutants that alter methylation and silencing of a densely methylated endogenous reporter gene, we recovered 11 loss-of-function alleles in the CMT3 chromomethylase gene. The cmt3 mutants displayed enhanced expression and reduced methylation of the reporter, particularly at non-CG cytosines. CNG methylation was also reduced at repetitive centromeric sequences. Thus, CMT3 is a key determinant for non-CG methylation. The lack of CMT homologs in animal genomes could account for the observation that in contrast to plants, animals maintain primarily CG methylation.