The ability to turn genes on and off and precisely adjust their expression levels is critical for all living organisms. It may be argued that this regulation is as important as the structures of proteins encoded by genes. Regulation of genome activity is a complex process and one of its critical components are non-coding RNAs (ncRNAs) – ribonucleic acids that do not encode proteins but perform various structural and regulatory functions. Our long term objective is to understand molecular mechanisms used to control genomes. We are especially focused on the roles of ncRNAs and how they affect organization of DNA into chromatin. We use plant model systems and an array of genetic, biochemical and genomic tools to investigate how ncRNAs control DNA methylation, nucleosome positioning and chromosome organization.