Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states
- Frederic Pontvianne1,2,9,12,
- Todd Blevins1,2,3,8,
- Chinmayi Chandrasekhara1,2,8,
- Iva Mozgová4,8,10,
- Christiane Hassel5,
- Olga M.F. Pontes6,
- Sarah Tucker7,11,
- Petr Mokroš4,
- Veronika Muchová4,
- Jiří Fajkus4 and
- Craig S. Pikaard1,2,3,12
- 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
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↵8 These authors contributed equally to this work.
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.
Keywords
- transcription
- gene silencing
- DNA methylation
- histone deacetylation
- chromatin assembly
- RNA polymerase I
- ribosomal RNA gene
Footnotes
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↵12 Corresponding authors
E-mail cpikaard{at}indiana.edu
E-mail frederic.pontvianne{at}univ-perp.fr
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Supplemental material is available for this article.
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Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.221648.113.
- Received May 9, 2013.
- Accepted June 14, 2013.
- Copyright © 2013 by Cold Spring Harbor Laboratory Press
Freely available online through the Genes & Development Open Access option.