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Literature DB >> 23873938

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

Frederic Pontvianne¹, Todd Blevins, Chinmayi Chandrasekhara, Iva Mozgová, Christiane Hassel, Olga M F Pontes, Sarah Tucker, Petr Mokros, Veronika Muchová, Jirí Fajkus, Craig S Pikaard.

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.

Entities: Chemical Gene Species

Keywords: DNA methylation; RNA polymerase I; chromatin assembly; gene silencing; histone deacetylation; ribosomal RNA gene; transcription

Mesh：

Substances：

Year: 2013 PMID： 23873938 PMCID： PMC3731543 DOI： 10.1101/gad.221648.113

Source DB: PubMed Journal: Genes Dev ISSN： 0890-9369 Impact factor: 11.361

28 in total

1. Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription.

Authors: R Santoro; I Grummt
Journal: Mol Cell Date: 2001-09 Impact factor: 17.970

2. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance.

Authors: Richard J Lawrence; Keith Earley; Olga Pontes; Manuela Silva; Z Jeffrey Chen; Nuno Neves; Wanda Viegas; Craig S Pikaard
Journal: Mol Cell Date: 2004-02-27 Impact factor: 17.970

3. Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana.

Authors: F Barneche; F Steinmetz; M Echeverría
Journal: J Biol Chem Date: 2000-09-01 Impact factor: 5.157

4. Visualization of nucleolar organizer regions im mammalian chromosomes using silver staining.

Authors: C Goodpasture; S E Bloom
Journal: Chromosoma Date: 1975-11-20 Impact factor: 4.316

5. In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes.

Authors: Sarah L French; Yvonne N Osheim; Francesco Cioci; Masayasu Nomura; Ann L Beyer
Journal: Mol Cell Biol Date: 2003-03 Impact factor: 4.272

6. RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase.

Authors: Joseph J Sandmeier; Sarah French; Yvonne Osheim; Wang L Cheung; Christopher M Gallo; Ann L Beyer; Jeffrey S Smith
Journal: EMBO J Date: 2002-09-16 Impact factor: 11.598

7. Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis.

Authors: Olga Pontes; Richard J Lawrence; Nuno Neves; Manuela Silva; Jae-Hyeok Lee; Z Jeffrey Chen; Wanda Viegas; Craig S Pikaard
Journal: Proc Natl Acad Sci U S A Date: 2003-09-22 Impact factor: 11.205

8. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats.

Authors: Aline V Probst; Mathilde Fagard; Florence Proux; Philippe Mourrain; Stéphanie Boutet; Keith Earley; Richard J Lawrence; Craig S Pikaard; Jane Murfett; Ian Furner; Hervé Vaucheret; Ortrun Mittelsten Scheid
Journal: Plant Cell Date: 2004-03-22 Impact factor: 11.277

9. Identification of Ag-NOR proteins, markers of proliferation related to ribosomal gene activity.

Authors: P Roussel; D Hernandez-Verdun
Journal: Exp Cell Res Date: 1994-10 Impact factor: 3.905

10. Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci.

Authors: Ana D Caperta; Nuno Neves; Leonor Morais-Cecílio; Rui Malhó; Wanda Viegas
Journal: J Cell Sci Date: 2002-07-15 Impact factor: 5.285

55 in total

1. Alu element-containing RNAs maintain nucleolar structure and function.

Authors: Maïwen Caudron-Herger; Teresa Pankert; Jeanette Seiler; Attila Németh; Renate Voit; Ingrid Grummt; Karsten Rippe
Journal: EMBO J Date: 2015-10-13 Impact factor: 11.598

2. The many faces of plant chromatin: Meeting summary of the 4th European workshop on plant chromatin 2015, Uppsala, Sweden.

Authors: Iva Mozgová; Claudia Köhler; Valérie Gaudin; Lars Hennig
Journal: Epigenetics Date: 2015 Impact factor: 4.528

10. HISTONE DEACETYLASE6-Defective Mutants Show Increased Expression and Acetylation of ENHANCER OF TRIPTYCHON AND CAPRICE1 and GLABRA2 with Small But Significant Effects on Root Epidermis Cellular Pattern.

Authors: Dong-Xu Li; Wen-Qian Chen; Zhi-Hong Xu; Shu-Nong Bai
Journal: Plant Physiol Date: 2015-07-04 Impact factor: 8.340

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

1. Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription.

2. A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance.

3. Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana.

4. Visualization of nucleolar organizer regions im mammalian chromosomes using silver staining.

5. In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes.

6. RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase.

7. Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis.

8. Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats.

9. Identification of Ag-NOR proteins, markers of proliferation related to ribosomal gene activity.

10. Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci.

1. Alu element-containing RNAs maintain nucleolar structure and function.

2. The many faces of plant chromatin: Meeting summary of the 4th European workshop on plant chromatin 2015, Uppsala, Sweden.

Review 3. Nucleolar DNA: the host and the guests.

Review 4. Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors.

5. Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis.

6. Selective nucleolus organizer inactivation in Arabidopsis is a chromosome position-effect phenomenon.

7. Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes.

Review 8. Plant nucleolar DNA: Green light shed on the role of Nucleolin in genome organization.

Review 9. Three-dimensional nuclear organization in Arabidopsis thaliana.

10. HISTONE DEACETYLASE6-Defective Mutants Show Increased Expression and Acetylation of ENHANCER OF TRIPTYCHON AND CAPRICE1 and GLABRA2 with Small But Significant Effects on Root Epidermis Cellular Pattern.