Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome

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 s...

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Main Authors: Frédéric Pontvianne, Marie-Christine Carpentier, Nathalie Durut, Veronika Pavlištová, Karin Jaške, Šárka Schořová, Hugues Parrinello, Marine Rohmer, Craig S. Pikaard, Miloslava Fojtová, Jiří Fajkus, Julio Sáez-Vásquez
Format: Article
Language:English
Published: Elsevier 2016-08-01
Series:Cell Reports
Subjects:
Online Access:http://www.sciencedirect.com/science/article/pii/S2211124716309020
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spelling doaj-a3b4c32aaf034e87ac41c535bfba579d2020-11-25T00:19:05ZengElsevierCell Reports2211-12472016-08-011661574158710.1016/j.celrep.2016.07.016Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana GenomeFrédéric Pontvianne0Marie-Christine Carpentier1Nathalie Durut2Veronika Pavlištová3Karin Jaške4Šárka Schořová5Hugues Parrinello6Marine Rohmer7Craig S. Pikaard8Miloslava Fojtová9Jiří Fajkus10Julio Sáez-Vásquez11CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, FranceCNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, FranceCNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, FranceCentral European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech RepublicCentral European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech RepublicCentral European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech RepublicMontpellier GenomiX, Montpellier Cedex 5, FranceMontpellier GenomiX, Montpellier Cedex 5, FranceDepartment of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USACentral European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech RepublicCentral European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech RepublicCNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, FranceThe 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.http://www.sciencedirect.com/science/article/pii/S2211124716309020nucleolusnuclear architecturetelomerenucleolus-associated chromatin domainsheterochromatin
collection DOAJ
language English
format Article
sources DOAJ
author Frédéric Pontvianne
Marie-Christine Carpentier
Nathalie Durut
Veronika Pavlištová
Karin Jaške
Šárka Schořová
Hugues Parrinello
Marine Rohmer
Craig S. Pikaard
Miloslava Fojtová
Jiří Fajkus
Julio Sáez-Vásquez
spellingShingle Frédéric Pontvianne
Marie-Christine Carpentier
Nathalie Durut
Veronika Pavlištová
Karin Jaške
Šárka Schořová
Hugues Parrinello
Marine Rohmer
Craig S. Pikaard
Miloslava Fojtová
Jiří Fajkus
Julio Sáez-Vásquez
Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome
Cell Reports
nucleolus
nuclear architecture
telomere
nucleolus-associated chromatin domains
heterochromatin
author_facet Frédéric Pontvianne
Marie-Christine Carpentier
Nathalie Durut
Veronika Pavlištová
Karin Jaške
Šárka Schořová
Hugues Parrinello
Marine Rohmer
Craig S. Pikaard
Miloslava Fojtová
Jiří Fajkus
Julio Sáez-Vásquez
author_sort Frédéric Pontvianne
title Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome
title_short Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome
title_full Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome
title_fullStr Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome
title_full_unstemmed Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome
title_sort identification of nucleolus-associated chromatin domains reveals a role for the nucleolus in 3d organization of the a. thaliana genome
publisher Elsevier
series Cell Reports
issn 2211-1247
publishDate 2016-08-01
description 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.
topic nucleolus
nuclear architecture
telomere
nucleolus-associated chromatin domains
heterochromatin
url http://www.sciencedirect.com/science/article/pii/S2211124716309020
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