The genes that encode ribosomal RNA exist in two distinct types of chromatin--an 'open' conformation that is permissive to transcription and a 'closed' conformation that is transcriptionally refractive. Recent studies have provided insights into the molecular mechanisms that silence either entire nucleolus organizer regions (NORs) in genetic hybrids or individual rRNA genes within a NOR. An emerging theme from these studies is that epigenetic mechanisms operating at the level of DNA methylation and histone modifications alter the chromatin structure and control the ratio of active and inactive rRNA genes.