Molecular Biology

A Guide to Silence

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Science  14 May 2004:
Vol. 304, Issue 5673, pp. 931
DOI: 10.1126/science.304.5673.931a

RNA-directed DNA methylation (RdDM) is an RNA silencing mechanism that so far appears to be specific to plants. RdDM requires a double-stranded RNA that is cut into short 21- to 26- nucleotide fragments, much like the small interfering RNAs seen in RNA interference (RNAi); DNA sequences homologous to these RNAs are then methylated and silenced. As well as being implicated in the methylation of protein-coding regions of genes subject to post-transcription gene silencing, RdDM is also involved in transcriptional gene silencing (TGS) through the RNA-directed methylation of promoter sequences.

Although several DNA methylases have been implicated in RdDM, it is still not known how RNA targets specific DNA sequences (as in RNAi). In order to delve deeper into the mechanism of RdDM, Kanno et al. have used a TGS-based screen to identify three complementation groups in Arabidopsis, one of which is the gene drd1. This gene is required for non-CpG methylation-based silencing in a target promoter and appears to act locally. It also has homology with SWI/SNF and Drosophila RAD54 chromatin remodeling proteins. Mutations in the various alleles of drd1 all map to conserved functionally important regions of DRD1's putative SWI/SNF ATPase domain, which in other SWI/SNF proteins is essential for remodeling. RAD54 is required for homologous DNA repair, and thus the authors speculate that DRD1 could aid in homology searching, clearing of chromatin, and heteroduplex formation that may guide DNA methylases. — GR

Curr. Biol. 14, 801 (2004).

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