The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified nucleolus-associated chromatin domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance.

Central European Institute of Technology and Faculty of Science Masaryk University 62500 Brno Czech Republic

CNRS Laboratoire Génome et Développement des Plantes UMR5096 66860 Perpignan France; Université de Perpignan Via Domitia Laboratoire Génome et Développement des Plantes UMR5096 66860 Perpignan France

CNRS Laboratoire Génome et Développement des Plantes UMR5096 66860 Perpignan France; Université de Perpignan Via Domitia Laboratoire Génome et Développement des Plantes UMR5096 66860 Perpignan France; Department of Biology and Department of Molecular and Cellular Biochemistry Indiana University Bloomington IN 47405 USA

Department of Biology and Department of Molecular and Cellular Biochemistry Indiana University Bloomington IN 47405 USA; Howard Hughes Medical Institute Indiana University Bloomington IN 47405 USA

Montpellier GenomiX Montpellier Cedex 5 France

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