Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states

Frederic Pontvianne; Todd Blevins; Chinmayi Chandrasekhara; Iva Mozgová; Christiane Hassel; Olga M.F. Pontes; Sarah Tucker; Petr Mokroš; Veronika Muchová; Jiří Fajkus; Craig S. Pikaard

doi:10.1101/gad.221648.113

Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states

¹Department of Biology,
²Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA;
³Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA;
⁴CEITEC-Central European Institute of Technology and Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic;
⁵Flow Cytometry Core Facility, Indiana University, Bloomington, Indiana 47405, USA;
⁶Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
⁷Division of Biology and Biomedical Sciences, Washington University, St. Louis, Missouri 63130, USA

↵8 These authors contributed equally to this work.

↵Present addresses: ⁹Laboratoire Genome et Developpement des Plantes, UMR 5096 CNRS-University of Perpignan via Domitia, Perpignan, France;
↵10 Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden;
↵11 Monsanto Company, St. Louis, MO 63107, USA

Abstract

Eukaryotes can have thousands of 45S ribosomal RNA (rRNA) genes, many of which are silenced during development. Using fluorescence-activated sorting techniques, we show that active rRNA genes in Arabidopsis thaliana are present within sorted nucleoli, whereas silenced rRNA genes are excluded. DNA methyltransferase (met1), histone deacetylase (hda6), or chromatin assembly (caf1) mutants that disrupt silencing abrogate this nucleoplasmic–nucleolar partitioning. Bisulfite sequencing data indicate that active nucleolar rRNA genes are nearly completely demethylated at promoter CGs, whereas silenced genes are nearly fully methylated. Collectively, the data reveal that rRNA genes occupy distinct but changeable nuclear territories according to their epigenetic state.

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Footnotes

↵12 Corresponding authors

E-mail cpikaard{at}indiana.edu

E-mail frederic.pontvianne{at}univ-perp.fr
Supplemental material is available for this article.
Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.221648.113.