RNA-mediated epigenetic regulation of gene expression involves diverse RNA classes, including small and long non-coding RNAs (lncRNAs), which regulate gene expression, genome stability, and defense against foreign genetic elements. Small RNAs modify chromatin structure and silence transcription by guiding Argonaute-containing complexes to complementary nascent RNA scaffolds, recruiting histone and DNA methyltransferases. Recent advances suggest that chromatin-associated lncRNAs also recruit chromatin-modifying complexes independently of small RNAs. These co-transcriptional silencing mechanisms form RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops. In many organisms, intergenic or antisense transcription produces small RNAs and lncRNAs that regulate chromatin structure. Small RNAs also modify chromatin and target gene expression via RNA interference (RNAi) pathways. Studies in the mustard plant Arabidopsis thaliana first demonstrated that post-transcriptional gene silencing and DNA methylation of target loci correlate with the production of small interfering RNAs (siRNAs), linking RNA-directed DNA methylation to the RNAi pathway. Studies in fission yeast, ciliate protozoa, and animal germline and somatic cells revealed a general role for RNAi and related mechanisms in heterochromatin formation or DNA methylation. RNA also regulates chromatin modifications and structure through pathways not involving RNAi. Some lncRNAs and even some mRNAs contain signals that recruit chromatin-modifying complexes independently of small RNAs. Early examples include Xinactive specific transcript (XIST), which coats the inactive X chromosome in female mammals, and RNA on the X 1 (roX1) and roX2, which coat the X chromosome in male flies, leading to increased transcription. More recently, a large number of other lncRNAs have been shown to act at a gene-specific level to either activate or silence transcription. A unifying mechanism by which small RNAs and lncRNAs modify chromatin structure and silence transcription is the formation of RNA scaffolds. Although the machineries that use RNA scaffolds have greatly diverged throughout evolution, key similarities enable defining common themes and principles conserved in eukaryotes from fission yeast to mammals. In this Review, we discuss recent progress in understanding the role of RNA in genome regulation, focusing on the roles of different classes of chromatin-bound RNAs as scaffolds for chromatin-modifying complexes. We also review recent mechanistic insights into how small-RNA amplification loops are coupled to histone or DNA methylation to form self-reinforcing positive feedback systems that maintain epigenetic states. We discuss how small RNAs and Argonaute (AGO) complexes are assembled and how they target specific chromatin regions for silencing, focusing on the better understood S. pombe and A. thaliana systemsRNA-mediated epigenetic regulation of gene expression involves diverse RNA classes, including small and long non-coding RNAs (lncRNAs), which regulate gene expression, genome stability, and defense against foreign genetic elements. Small RNAs modify chromatin structure and silence transcription by guiding Argonaute-containing complexes to complementary nascent RNA scaffolds, recruiting histone and DNA methyltransferases. Recent advances suggest that chromatin-associated lncRNAs also recruit chromatin-modifying complexes independently of small RNAs. These co-transcriptional silencing mechanisms form RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops. In many organisms, intergenic or antisense transcription produces small RNAs and lncRNAs that regulate chromatin structure. Small RNAs also modify chromatin and target gene expression via RNA interference (RNAi) pathways. Studies in the mustard plant Arabidopsis thaliana first demonstrated that post-transcriptional gene silencing and DNA methylation of target loci correlate with the production of small interfering RNAs (siRNAs), linking RNA-directed DNA methylation to the RNAi pathway. Studies in fission yeast, ciliate protozoa, and animal germline and somatic cells revealed a general role for RNAi and related mechanisms in heterochromatin formation or DNA methylation. RNA also regulates chromatin modifications and structure through pathways not involving RNAi. Some lncRNAs and even some mRNAs contain signals that recruit chromatin-modifying complexes independently of small RNAs. Early examples include Xinactive specific transcript (XIST), which coats the inactive X chromosome in female mammals, and RNA on the X 1 (roX1) and roX2, which coat the X chromosome in male flies, leading to increased transcription. More recently, a large number of other lncRNAs have been shown to act at a gene-specific level to either activate or silence transcription. A unifying mechanism by which small RNAs and lncRNAs modify chromatin structure and silence transcription is the formation of RNA scaffolds. Although the machineries that use RNA scaffolds have greatly diverged throughout evolution, key similarities enable defining common themes and principles conserved in eukaryotes from fission yeast to mammals. In this Review, we discuss recent progress in understanding the role of RNA in genome regulation, focusing on the roles of different classes of chromatin-bound RNAs as scaffolds for chromatin-modifying complexes. We also review recent mechanistic insights into how small-RNA amplification loops are coupled to histone or DNA methylation to form self-reinforcing positive feedback systems that maintain epigenetic states. We discuss how small RNAs and Argonaute (AGO) complexes are assembled and how they target specific chromatin regions for silencing, focusing on the better understood S. pombe and A. thaliana systems