Science 297(5588): 1818-1819 (Sept 2002)
RNAi and Heterochromatin—a Hushed-Up Affair
Robin Allshire

Sometimes it is necessary to silence genes, a process that involves shutting down regions of active chromatin. Genes can be silenced by methylation of lysine 9 in histone H3 of chromatin, but RNAi also turns out to be important in chromatin-based gene silencing. In a Perspective, Robin Allshire discusses new work (Volpe et al.) that shows how RNAi is able to shut down chromatin in fission yeast by promoting H3 lysine 9 methylation, perhaps by altering the recruitment of enzymes that methylate DNA and histones.

The highly repetitive DNA (heterochromatin) of eukaryotic genomes contains a large number of repeats and transposons. Regions of heterochromatin are frequently associated with centromeres, which are crucial for the segregation of chromosomes during cell division. Transgenes inserted into heterochromatin domains can be shut down through the influence of silent chromatin in this region. The formation of silent chromatin requires that histone H3 of chromatin be deacetylated and then methylated on lysine 9. The methylated lysine 9 residue binds to heterochromatin protein 1 (Swi6 in fission yeast), leading to a block in transcription. Subsequent methylation of the DNA in this region then locks the chromatin into the silent state (1). Genes can also be silenced at the RNA level by RNA interference (RNAi), which depends on the accidental or deliberate expression of double-stranded RNAs (dsRNAs). These dsRNAs are processed and amplified into small interfering RNAs (siNAs) that bind to and degrade any mRNA transcripts with the same sequence, resulting in loss of expression of the genes encoding these mRNAs (2). Although seemingly separate mechanisms, H3 lysine 9 methylation and RNAi were recently found to be part of the same gene-silencing pathway in the fission yeast Schizosaccharomyces pombe. This unexpected discovery is providing new insights into how different forms of chromatin silencing may be triggered.

Keeping chromatin quiet.
Top- and bottom-strand RNA transcripts from the outer centromeric DNA repeats of S. pombe. These overlapping RNAs form dsRNAs, which are diced and processed by Argonaute (Ago1), Dicer (Dcr1), and RNA-dependent RNA polymerase (Rdp1) into siRNAs capable of silencing genes. The siRNAs may activate or recruit chromatin-modifying enzymes that promote methylation of lysine 9 in histone H3, allowing the binding of Swi6 to chromatin and the formation of silenced chromatin. This results in repression of top-strand synthesis, although bottom-strand transcription and processing still persist in silent chromatin. Stochastic loss of gene silencing results in production of the top-strand RNA, which immediately anneals to the bottom-strand RNA. This provides dsRNAs for amplification by Rdp1 and cleavage by Dcr1, resulting in regeneration of siRNAs. Annealing of siRNAs via the Ago1/RISC complex may allow Rdp1 to transiently produce more extensive dsRNAs (and thus siRNAs) by lateral spreading both upstream and downstream of where the dsRNAs predominate. This would result in chromatin modifications that spread outward from the region where Rdp1 is associated with chromatin and where abundant siRNAs are generated [see (8)].

Imprinting, Disruptive Selection, Antithetical Dominance