The nucleolus — the site of rRNA gene transcription and ribosome biogenesis — is the largest nuclear body. Pontvianne et al. identified nucleolus-associated chromatin domains (NADs) in plants. Nucleoli were purified from Arabidopsis thaliana leaves and DNA sequencing revealed that, in addition to actively transcribed rRNA genes, NADs contain heterochromatic regions and include transposable elements, sub-telomeric regions, silenced protein-coding genes, tRNA genes and pseudogenes. In nucleolin 1 mutants, in which the nucleolar structure is disrupted, NAD composition was altered. rRNA genes on chromosome 2 became abnormally activated and associated with the nucleolus and nucleolar clustering of telomeres was affected. Moreover, telomeres were shorter. This work suggests a functional role for the nucleoulus in genome organization and telomere maintenance.