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nce ust Review TRENDS in Plant Science Vol.12 No.2expression, genome organization and plant development [2,4–7]. In plants, most 5-methylcytosines are associated with heterochromatic, transcriptionally inactive regions, which are often enriched with repetitive DNA sequences. Yet, in Arabidopsis thaliana, the genome-wide high-resolution mapping of DNA methylation has recently revealed that over one-third of expressed genes contain methylations within the transcribed regions [8]. Whereas, in animals, cytosine methylation is prevalent in symmetrical CpG dinucleotides, in plants, it is often found in symmetrical CpG and CpNpG as well as in non-symmetrical CpHpH (H = C, A or T) contexts [9,10]. A growing body of evidence suggests that cytosine meth-ylation at specific chromosomal domains is triggered by RNA molecules (i.e. small interfering RNAs) in a mech-anism known as RNA-dependent DNA methylation (RdDM) [11–13]. were characterized in a variety of plant species including corn, wheat and carrot [19,20]. In nuclear extracts of carrot (Daucus carota), two classes of MBPs were ident-ified: (i) dcMBP1, which showed high affinity for 5-methylcytosine in CpG context, and (ii) dcMBP2, which showed high affinity for 5-methylcytosine in CpNpG and CpHpH contexts [20]; none of these MBPs have been isolated and characterized. Great progress in identifying plant MBP-encoding genes (i.e. MBD proteins) was made with the release of various plant genome and EST sequences. Based on amino acid sequence homology with animal MBDs (Box 1) (reviewed in Ref. [21]), the Plant Chromatin databas