Odd genetic observations in the 1980s and 1990s indicated that RNA may play a general role in regulating gene expression, when it was reported that both sense and antisense RNAs could modulate gene expression transcriptionally and post-transcriptionally, referred to as ‘co-suppression’, ‘gene silencing’ or ‘RNA interference’ (RNAi). The finding that introducing sense and antisense RNAs together resulted in systemic silencing of target genes led to the dissection of the RNAi pathways, showing that dsRNA precursors are processed to form small RNAs that guide DNA methylation and cleavage of orthologous sequences in mRNAs. It was soon discovered that these pathways are used extensively to control gene expression during differentiation and development via ‘microRNAs’ (miRNAs) derived from introns and other non-protein-coding transcripts, the numbers of which increased during animal evolution. Similar regulatory RNA pathways were characterized in plants. Related small RNAs, ‘piRNAs’, were found to be required for germ and stem cell development in animals, some of which are produced from transposon-derived sequences. Other classes of small regulatory RNAs were found to be generated from tRNAs, rRNAs, snoRNAs, snRNAs, gene promoters and splice junctions, and small RNAs were shown to mediate intergenerational and interspecies communication. A related pathway, termed ‘CRISPR’, was found to target cleavage of bacteriophage genomes, manipulation of which has revolutionized genetic analysis and genetic engineering. Both CRISPR and RNAi use RNAs to guide generic effector proteins sequence-specifically to target RNAs and DNAs, a highly efficient and flexible system of gene control.