This review article—co-written with Jim Birchler of the Department of Biological Sciences at the University of Missouri-Columbia in Columbia, Missouri—is the first to provide equal and comprehensive coverage to all four currently known RNAi-mediated pathways in the nucleus.

“It has been amazing to find over the years that homology-dependent gene silencing is a variant of what we now call RNAi.”

Previous reviews on similar topics concentrated on only one or two pathways —usually on RNAi-mediated heterochromatin formation in fission yeast. Our review covered, in addition, RNA-directed DNA methylation in plants, meiotic silencing of unpaired DNA in Neurospora, and RNAi-mediated DNA elimination in ciliated protozoa.

It was initially thought that RNAi would act exclusively in the cytoplasm to degrade mRNA. The realization that the RNAi machinery also has a major role in guiding epigenetic modifications in the nucleus constituted a major advance in gene silencing research.

The use of short RNAs generated by the RNAi machinery to target DNA and histone methylation to matching sequences in the genome permits these modifications to be induced in a highly sequence-specific manner. Some groups are now using promoter-directed short RNAs as an alternative to "classical" RNAi to elicit gene silencing for functional genomics.

In all organisms, gene activity must be carefully regulated so that each cell type expresses only a subset of genes while the rest of the genes remain silent. How is silencing targeted to specific genes? Whereas previous ideas and experiments focused on regulatory proteins, our review describes recent findings demonstrating an unanticipated role for tiny regulatory RNAs in targeting genes that have a matching sequence for silencing.

Our lab has a long history of gene silencing research in plants, beginning with our work in 1989 on "homology-dependent gene silencing," which appeared to be induced by sequence-specific interactions between identical promoter elements.

Later, we learned that this silencing phenomenon is triggered by double-stranded RNAs containing promoter sequences. It has been amazing to find over the years that homology-dependent gene silencing is a variant of what we now call RNAi.