RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

Key Points Small RNAs with roles in the nucleus include those that are generated mainly by Dicer proteins and loaded into Argonaute proteins (small interfering RNAs (siRNAs)) and also those that are Dicer-independent (largely generated by the ping-pong cycle) and are loaded into PIWI proteins (PIWI-interacting RNAs (piRNAs)). The subcellular localization where siRNA biogenesis occurs is variable among organisms. However, cytoplasmic Argonaute loading might be conserved. Nuclear RNA interference (RNAi) directs heterochromatic modifications at target loci including methylation of histone H3 at lysine 9 (H3K9; in Schizosaccharomyces pombe ) and DNA methylation (in Arabidopsis thaliana ). These reduce transcription, facilitating transcriptional gene silencing (TGS). Examples in A. thaliana and S. pombe show that transcription by RNA polymerase is required to produce nascent RNA that is targeted by nuclear RNAi; this process is termed co-transcriptional gene silencing (CTGS). There is evidence in the somatic cells of metazoans that endogenous siRNA pathways are involved in co-transcriptional regulation and heterochromatin formation, suggesting a conserved nuclear role for RNAi. RNAi has a crucial germline role in silencing transposons both post-transcriptionally and transcriptionally. In both metazoans and plants, transposons are revealed for transcription and produce small RNAs that target transposons in the germ cells to maintain silencing through nuclear RNAi. In mammals, piRNAs can direct de novo cytosine methylation in the germ line and have been shown to do so at an imprinted locus. This suggests that nuclear RNAi might have another conserved role in parent-of-origin imprinting. The piRNAs of Caenorhabditis elegans (21U small RNAs) can direct transcriptional silencing by H3K9 methylation in the germ line that is heritable and dependent on nuclear RNAi (NRDE) pathway members. Roles are emerging for small RNAs in DNA repair and genome maintenance, through both the maintenance and regulation of heterochromatic domains (such as centromeres and telomeres) and through direct involvement in DNA repair: for example, at double-strand breaks. In addition to well-known roles in the cytoplasm, a growing number of functions for small RNAs in the nucleus are being discovered. These include roles in transcriptional repression, epigenetic modifications and genome stability. This Review considers examples from animals, plants and fungi. A growing number of functions are e