Background

Heterochromatin, highly condensed chromosomal DNA associ-ated with repetitive sequences and transposons, appears to play important roles in nuclear processes such as chromosomal seg-regation and genomic stability.1-3 Studies from fission yeast and plants have demonstrated a role for small RNA in heterochroma-tin formation and maintenance.4-7 In the plant silencing mecha-nism called RNA-directed DNA methylation (RdDM), siRNA directs de novo cytosine methylation at homologous DNA regions.8,9 These RNA-based silencing mechanisms provide an important level of epigenetic control to repress transposable ele-ments (TEs) and aberrant genes such as transgenes, while also playing a role to regulate the expression of endogenous genes. In plants, two nuclear DNA-dependent RNA polymer-ases have evolved to work exclusively in RNA-mediated silenc-ing pathways.10 DNA-dependent RNA polymerases IV and