,
, , p.1
, Characterization of AtNUC-L1 Reveals a Central Role of Nucleolin in Nucleolus Organization and Silencing of AtNUC-L2 Gene in Arabidopsis, Mol. Biol. Cell, vol.18, pp.369-379, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00164253
, Characterization of a ribonuclease III-like protein required for cleavage of the pre-rRNA in the 3'ETS in Arabidopsis, Nucleic Acids Research, vol.36, pp.1163-1175, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02121738
, Identification of protein factors and U3 snoRNAs from a B.oleracea RNP complex involved in processing of pre-rRNA, Plant J, issue.3, pp.383-398, 2010.
, Nucleolin Is Required for DNA Methylation State and the Expression of rRNA Gene Variants in Arabidopsis thaliana, PLoS Genet. Nov, vol.24, issue.11, p.1001225, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00787644
, Two distinct RdDM-like pathways are required for proper rRNA gene dosage in A. thaliana
, Chromosome-specific NOR inactivation accounts for selective rRNA gene silencing and dosage control in Arabidopsis, Genes & Development, vol.30, p.352, 2015.
, Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I-and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit, Nucleic Acids Research Apr, vol.30, issue.8, pp.4163-78, 2015.
, A two-step process for epigenetic inheritance in Arabidopsis, Molecular Cell. Apr, vol.10, issue.1, pp.30-42, 2014.
, Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states, Genes & Development, vol.27, pp.1545-1550, 2013.
, Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis, Genes & Development, vol.26, pp.945-957, 2012.
, Arabidopsis Histone Lysine Methyltransferases, Adv. In Bot. Res. Jan, vol.53, pp.1-22, 2010.
, Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation, Genes & Development, vol.24, pp.1119-1132, 2010.
, Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin, EMBO J, vol.19, pp.6870-6881, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00023725
, Solution structure of the two N-terminal RNAbinding domains of nucleolin and NMR study of the interaction with its RNA target, J Mol Biol, vol.303, pp.227-241, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00023726
, A Polycomb-based switch underlying quantitative epigenetic memory, Nature, vol.476, pp.105-108, 2011.
, A glucocorticoid-mediated transcriptional induction system in transgenic plants, Plant J Cell Mol Biol, vol.11, pp.605-612, 1997.
, Nucleolus-associated telomere clustering and pairing precede meiotic chromosome synapsis in Arabidopsis thaliana, J Cell Sci, vol.114, pp.4207-4217, 2001.
, Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA, Mol Cell, vol.45, pp.147-157, 2012.
, The nucleolar detention pathway: A cellular strategy for regulating molecular networks, Cell Cycle Georget Tex, vol.11, pp.2059-2062, 2012.
, Changes of telomere length cause reciprocal changes in the lifespan of mother cells in Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, vol.94, pp.9768-9772, 1997.
, Bacterial chromosome organization and segregation, Annu Rev Cell Dev Biol, vol.31, pp.171-199, 2015.
,
, Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila, Cell, vol.144, pp.214-226
, Hi-C: a comprehensive technique to capture the conformation of genomes, Methods San Diego Calif, vol.58, pp.268-276, 2012.
, Heterochromatin dynamics during developmental transitions in Arabidopsis -a focus on ribosomal DNA loci, Gene, vol.526, pp.39-45, 2013.
,
, High-resolution statistical mapping reveals gene territories in live yeast, Nat Methods, vol.5, pp.1031-1037
, Environmental perception and epigenetic memory: mechanistic insight through FLC, Plant J Cell Mol Biol, vol.83, pp.133-148, 2015.
, Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance, 2015.
, Genome architecture: domain organization of interphase chromosomes, Cell, vol.152, pp.1270-1284, 2013.
, Heterosis. Plant Cell, vol.22, pp.2105-2112, 2010.
, A two-step process for epigenetic inheritance in Arabidopsis, Mol Cell, vol.54, pp.30-42, 2014.
, The multifunctional nucleolus, Nat Rev Mol Cell Biol, vol.8, pp.574-585, 2007.
, Inducible gene expression systems for plants, Methods Mol Biol Clifton NJ, vol.655, pp.65-75, 2010.
, The movement of coiled bodies visualized in living plant cells by the green fluorescent protein, Mol Biol Cell, vol.10, pp.2297-2307, 1999.
, The nucleolus under stress, Mol Cell, vol.40, pp.216-227, 2010.
, Light signaling controls nuclear architecture reorganization during seedling establishment, Proc Natl Acad Sci U S A, vol.112, pp.2836-2844, 2015.
, Recognition of pre-formed and flexible elements of an RNA stem-loop by nucleolin, J Mol Biol, vol.309, pp.763-775, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00023732
, Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes, Proc Natl Acad Sci U S A, vol.108, pp.4334-4339, 2011.
, High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation, Plant Cell, vol.23, pp.873-894, 2011.
, Accounting for technical noise in single-cell RNA-seq experiments, Nat Methods, vol.10, pp.1093-1095, 2013.
, Ferritins and iron storage in plants, Biochim Biophys Acta, vol.1800, pp.806-814, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00507415
, ABSENCE OF RIBOSOMAL RNA SYNTHESIS IN THE ANUCLEOLATE MUTANT OF XENOPUS LAEVIS, Proc Natl Acad Sci, vol.51, pp.139-146, 1964.
, To be or not to be in the nucleolus, Nat Cell Biol, vol.2, pp.107-112, 2000.
, Depletion of the yeast nuclear exosome subunit Rrp6 results in accumulation of polyadenylated RNAs in a discrete domain within the nucleolus, Mol Cell Biol, vol.27, pp.4157-4165, 2007.
, Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization, Cell, vol.117, pp.427-439, 2004.
, Alu elementcontaining RNAs maintain nucleolar structure and function, EMBO J, vol.34, pp.2758-2774, 2015.
, Chromosomespecific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis, Genes Dev, vol.30, pp.177-190, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01313216
, Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system, Cell, vol.155, pp.1479-1491, 2013.
, Arabidopsis HEMERA/pTAC12 initiates photomorphogenesis by phytochromes, Cell, vol.141, pp.1230-1240, 2010.
, Characterization of the requirements for localization of phytochrome B to nuclear bodies, Proc Natl Acad Sci, vol.100, pp.14493-14498, 2003.
, Genomic and epigenetic insights into the molecular bases of heterosis, Nat Rev Genet, vol.14, pp.471-482, 2013.
, Molecular mechanisms of polyploidy and hybrid vigor, Trends Plant Sci, vol.15, pp.57-71, 2010.
, Real-time dynamics of RNA polymerase II clustering in live human cells, Science, vol.341, pp.664-667, 2013.
, A distant coilin homologue is required for the formation of cajal bodies in Arabidopsis, Mol Biol Cell, vol.17, pp.2942-2951, 2006.
, Characterization of a ribonuclease III-like protein required for cleavage of the pre-rRNA in the 3'ETS in Arabidopsis, Nucleic Acids Res, vol.36, pp.1163-1175, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02121738
, The organization of replication and transcription, Science, vol.284, pp.1790-1795, 1999.
, RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4, Plant J Cell Mol Biol, vol.9, pp.259-272, 1996.
,
, Metal movement within the plant: contribution of nicotianamine and yellow stripe, Ann Bot, vol.103, pp.1-11
, Capturing chromosome conformation, Science, vol.295, pp.1306-1311, 2002.
, Nucleolar activation and vacuolation in embryo radicle cells during early germination, J Cell Sci, vol.76, pp.67-83, 1985.
, Controlling gene expression in response to stress, Nat Rev Genet, vol.12, pp.833-845, 2011.
, Ultrastructural cytochemistry of the mammalian cell nucleolus, J Histochem Cytochem Off J Histochem Soc, vol.38, pp.1237-1256, 1990.
, Connecting the transcription site to the nuclear pore: a multi-tether process that regulates gene expression, J Cell Sci, vol.123, pp.1989-1999, 2010.
, Cell identity mediates the response of Arabidopsis roots to abiotic stress, Science, vol.320, pp.942-945, 2008.
, LITTLE NUCLEI genes affecting nuclear morphology in Arabidopsis thaliana, Plant Cell, vol.19, pp.2793-2803, 2007.
, A duplicated NUCLEOLIN gene with antagonistic activity is required for chromatin organization of silent 45S rDNA in Arabidopsis, Plant Cell, vol.26, pp.1330-1344, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02116071
, Nucleolin: dual roles in rDNA chromatin transcription, Gene, vol.556, pp.7-12, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02116040
, Chromatin dynamics of plant telomeres and ribosomal genes, Plant J Cell Mol Biol, vol.83, pp.18-37, 2015.
, Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation, Genes Dev, vol.24, pp.1119-1132, 2010.
, Quantification of cell identity from singlecell gene expression profiles, Genome Biol, vol.16, p.9, 2015.
, Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development, Dev Camb Engl, vol.133, pp.4163-4172, 2006.
, Nucleation by rRNA Dictates the Precision of Nucleolus Assembly, Curr Biol CB, vol.26, pp.277-285, 2016.
, High resolution autoradiography studies on chromatin functions, pp.3-53, 1978.
, Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis, Mol Biol Cell, vol.15, pp.2664-2673, 2004.
, Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants, Curr Biol CB, vol.17, pp.818-823, 2007.
, Light-regulated gene repositioning in Arabidopsis, Nat Commun, vol.5, p.3027, 2014.
, Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Casinduced gene modifications in Arabidopsis, Proc Natl Acad Sci U S A, vol.111, pp.4632-4637, 2014.
, AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins, Mol Cell Proteomics MCP, vol.9, pp.1063-1084, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00470319
, Systematic protein location mapping reveals five principal chromatin types in Drosophila cells, Cell, vol.143, pp.212-224, 2010.
, Considering transposable element diversification in de novo annotation approaches, PloS One, vol.6, p.16526, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00568705
, 1781. traité sur le venin de la vipère, avec des observations sur la structure primitive du corps animale
, Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate, Proc Natl Acad Sci U S A, vol.99, pp.14584-14589, 2002.
, The centennial of the Cajal body, Nat Rev Mol Cell Biol, vol.4, pp.975-980, 2003.
, Nucleolar factors direct the 2'-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA, Mol Cell Biol, vol.19, pp.6906-6917, 1999.
, The hierarchy of the 3D genome, Mol Cell, vol.49, pp.773-782, 2013.
, Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing, Curr Opin Cell Biol, vol.17, pp.281-286, 2005.
, Nuclear envelope dynamics during plant cell division suggest common mechanisms between kingdoms, Biochem J, vol.435, pp.661-667, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00586467
, Plant SUN domain proteins: components of putative plant LINC complexes?, Plant Signal Behav, vol.5, pp.154-156, 2010.
, Iron in seeds -loading pathways and subcellular localization, Front Plant Sci, vol.4, p.535, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01048736
, Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division, Genes Dev, vol.28, pp.220-230, 2014.
, Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture, Genome Biol, vol.14, p.129, 2013.
, Epigenetic control of RNA polymerase I transcription in mammalian cells, Biochim Biophys Acta, vol.1829, pp.393-404, 2013.
, Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions, Nature, vol.453, pp.948-951, 2008.
, Spatial reorganization of telomeres in long-lived quiescent cells, Genome Biol, vol.16, p.206, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01206018
, Localization of modified nucleotides in Schizosaccharomyces pombe spliceosomal small nuclear RNAs: modified nucleotides are clustered in functionally important regions, RNA N Y N, vol.2, pp.909-918, 1996.
, Isolation of nucleoli, Curr Protoc Cell Biol Editor Board Juan Bonifacino Al Chapter, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00709427
, Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes, Genes Dev, vol.22, pp.2204-2214, 2008.
, CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing, Nat Struct Mol Biol, vol.20, pp.1358-1366, 2013.
, Molecular analysis of telomere fusions in Arabidopsis: multiple pathways for chromosome end-joining, EMBO J, vol.23, pp.2304-2313, 2004.
, The ins and outs of gene regulation and chromosome territory organisation, Curr Opin Cell Biol, vol.19, pp.311-316, 2007.
, Nukleolen und Chromosomen in der Gattung Vicia, Planta, vol.15, pp.495-505, 1931.
, Assembly and disassembly of the nucleolus during the cell cycle, Nucl Austin Tex, vol.2, pp.189-194, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00666117
, Emerging concepts of nucleolar assembly, J Cell Sci, vol.115, pp.2265-2270, 2002.
, RNA viruses: hijacking the dynamic nucleolus, Nat Rev Microbiol, vol.5, pp.119-127, 2007.
, Nucleolar proteomics and viral infection, Proteomics, vol.10, pp.4077-4086, 2010.
, The many pathways of RNA degradation, Cell, vol.136, pp.763-776, 2009.
, Three-dimensional reconstructions of nucleolus-organizing regions in, Biol Cell Auspices Eur Cell Biol Organ, vol.66, pp.225-233, 1989.
, Abundance of ribosomal RNA gene copies maintains genome integrity, Science, vol.327, pp.693-696, 2010.
, Control of transposable elements in Arabidopsis thaliana, Chromosome Res Int J Mol Supramol Evol Asp Chromosome Biol, vol.22, pp.217-223, 2014.
, Environmental cues induce a long noncoding RNA-dependent remodeling of the nucleolus, Mol Biol Cell, vol.24, pp.2943-2953, 2013.
, ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing, Nat Struct Mol Biol, vol.16, pp.763-768, 2009.
, Cell cycle-dependent recruitment of telomerase RNA and Cajal bodies to human telomeres, Mol Biol Cell, vol.17, pp.944-954, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00021198
, Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice, Nucleic Acids Res, vol.41, p.188, 2013.
, Telomeres, the nucleolus and aging, Curr Opin Cell Biol, vol.10, pp.332-338, 1998.
, Dyskerin is a component of the Arabidopsis telomerase RNP required for telomere maintenance, Mol Cell Biol, vol.28, pp.2332-2341, 2008.
, Comprehensive analysis of the chromatin landscape in Drosophila melanogaster, Nature, vol.471, pp.480-485, 2011.
,
, Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus, Plant Cell, vol.21, pp.2045-2057
, Interaction of a plant virus-encoded protein with the major nucleolar protein fibrillarin is required for systemic virus infection, Proc Natl Acad Sci U S A, vol.104, pp.11115-11120, 2007.
, Cajal bodies and the nucleolus are required for a plant virus systemic infection, EMBO J, vol.26, pp.2169-2179, 2007.
, Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells, Cell, vol.163, pp.134-147, 2015.
, Single-cell dynamics of genome-nuclear lamina interactions, Cell, vol.153, pp.178-192, 2013.
, Chromatin modifications and their function, Cell, vol.128, pp.693-705, 2007.
, Degradation of a polyadenylated rRNA maturation by-product involves one of the three RRP6-like proteins in Arabidopsis thaliana, Mol Cell Biol, vol.28, pp.3038-3044, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00309545
, The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana, PLoS Genet, vol.10, p.1004564, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01067729
, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-359, 2012.
, Catalytically active telomerase holoenzyme is assembled in the dense fibrillar component of the nucleolus during S phase, Histochem Cell Biol, vol.141, pp.137-152, 2014.
, Arabidopsis CBF5 interacts with the H/ACA snoRNP assembly factor NAF1, Plant Mol Biol, vol.65, pp.615-626, 2007.
, An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana, Cell, vol.126, pp.93-106, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00164266
, Widespread rearrangement of 3D chromatin organization underlies polycombmediated stress-induced silencing, Mol Cell, vol.58, pp.216-231, 2015.
, Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model, Mol Biol Cell, vol.25, pp.1366-1373, 2014.
, Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation, Nat Rev Genet, vol.9, pp.583-593, 2008.
, Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets, Biol Direct, vol.8, p.6, 2013.
, DNA binding within the nucleosome core, Curr Opin Struct Biol, vol.8, pp.33-40, 1998.
, Recruitment of RPL11 at promoter sites of p53-regulated genes upon nucleolar stress through NEDD8 and in an Mdm2-dependent manner, Oncogene, vol.31, pp.3060-3071, 2012.
, UBF-binding site arrays form pseudoNORs and sequester the RNA polymerase I transcription machinery, Genes Dev, vol.19, pp.50-64, 2005.
, Biogenesis and function of nuclear bodies, Trends Genet TIG, vol.27, pp.295-306, 2011.
, Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis, Plant Cell, vol.15, pp.2929-2939, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01917210
, RNA-mediated chromatin-based silencing in plants, Curr Opin Cell Biol, vol.21, pp.367-376, 2009.
, The relationship of a particular chromosomal element to the development of the nucleoli in Zea mays, Zeit Zellforsch Mik Anat, vol.21, pp.294-328, 1934.
, The epigenetics of rRNA genes: from molecular to chromosome biology, Annu Rev Cell Dev Biol, vol.24, pp.131-157, 2008.
, Building silent compartments at the nuclear periphery: a recurrent theme, Curr Opin Genet Dev, vol.23, pp.96-103, 2013.
, Gateway-compatible tissue-specific vectors for plant transformation, BMC Res Notes, vol.8, p.63, 2015.
, Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation, Mol Cell Proteomics MCP, vol.10, 2011.
, Transactivated and chemically inducible gene expression in plants, Plant J Cell Mol Biol, vol.45, pp.651-683, 2006.
, Nucleolar Ultrastructure in Vertebrates, The Nucleolus, pp.10-20
, Dysfunction of chromatin assembly factor 1 induces shortening of telomeres and loss of 45S rDNA in Arabidopsis thaliana, Plant Cell, vol.22, pp.2768-2780, 2010.
,
, Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis, Proc Natl Acad Sci U S A, vol.106, pp.18843-18848
, Initial genomics of the human nucleolus, PLoS Genet, vol.6, p.1000889, 2010.
, Genome organization in and around the nucleolus, Trends Genet TIG, vol.27, pp.149-156, 2011.
, Localization of nucleolar phosphoproteins B23 and C23 during mitosis, Exp Cell Res, vol.146, pp.139-149, 1983.
, Nucleologenesis: composition and fate of prenucleolar bodies, Chromosoma, vol.92, pp.330-336, 1985.
, The nucleoplasmin homolog NLP mediates centromere clustering and anchoring to the nucleolus, Mol Cell, vol.50, pp.236-249, 2013.
, Transcription factories: genome organization and gene regulation, Chem Rev, vol.113, pp.8683-8705, 2013.
, Ribosomal DNA deletions modulate genome-wide gene expression: "rDNA-sensitive" genes and natural variation, PLoS Genet, vol.7, p.1001376, 2011.
, Ribosomal DNA contributes to global chromatin regulation, Proc Natl Acad Sci U S A, vol.106, pp.17829-17834, 2009.
, Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth, J Exp Bot, vol.65, pp.6057-6067, 2014.
, Chromosome territory arrangement and homologous pairing in nuclei of Arabidopsis thaliana are predominantly random except for NOR-bearing chromosomes, Chromosoma, vol.113, pp.258-269, 2004.
, The nucleolus, Cold Spring Harb Perspect Biol, vol.3, 2011.
, Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions, Mol Biol Cell, vol.16, pp.260-269, 2005.
, tRNA biology charges to the front, Genes Dev, vol.24, pp.1832-1860, 2010.
, Epigenetic regulation in plants, Cold Spring Harb Perspect Biol, vol.6, p.19315, 2014.
, Recent advances in X-chromosome inactivation research, Curr Opin Cell Biol, vol.24, pp.825-832, 2012.
, Three-dimensional genome architecture: players and mechanisms, Nat Rev Mol Cell Biol, vol.16, pp.245-257, 2015.
, The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center, Cell, vol.126, pp.79-92, 2006.
, siRNA and miRNA processing: new functions for Cajal bodies, Curr Opin Genet Dev, vol.18, pp.197-203, 2008.
, Intersection of small RNA pathways in Arabidopsis thaliana sub-nuclear domains, PloS One, vol.8, p.65652, 2013.
, Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana, PLoS Genet, vol.6, p.1001225, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00787644
, Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis, Genes Dev, vol.26, pp.945-957, 2012.
, Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states, Genes Dev, vol.27, pp.1545-1550, 2013.
, Arabidopsis Histone Lysine Methyltransferases, Adv Bot Res, vol.53, pp.1-22, 2010.
, Characterization of AtNUC-L1 reveals a central role of nucleolin in nucleolus organization and silencing of AtNUC-L2 gene in Arabidopsis, Mol Biol Cell, vol.18, pp.369-379, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00164253
, Mod5 protein binds to tRNA gene complexes and affects local transcriptional silencing, Proc Natl Acad Sci U S A, vol.110, pp.3081-3089, 2013.
, Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins, Mol Cell, vol.32, pp.673-684, 2008.
, rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch, Biochim Biophys Acta, vol.1769, pp.383-392, 2007.
, Recruitment of factors linking transcription and processing of prerRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells, Genes Dev, vol.21, pp.2041-2054, 2007.
, Study of the localization of iron, ferritin, and hemosiderin in Alzheimer's disease hippocampus by analytical microscopy at the subcellular level, J Struct Biol, vol.153, pp.42-54, 2006.
, Control of nuclear and nucleolar localization of nuclear inclusion protein a of picorna-like Potato virus A in Nicotiana species, Plant Cell, vol.21, pp.2485-2502, 2009.
, New insights into nucleolar architecture and activity, Int Rev Cytol, vol.255, pp.177-235, 2006.
, The nucleolar structure in plant cells, Revis Sobre Biol Cel RBC, vol.7, pp.1-154, 1986.
, LOCALIZATION OF DNA COMPLEMENTARY TO RIBOSOMAL RNA IN THE NUCLEOLUS ORGANIZER REGION OF DROSOPHILA MELANOGASTER, Proc Natl Acad Sci U S A, vol.53, pp.737-745, 1965.
, Physical clustering of FLC alleles during Polycomb-mediated epigenetic silencing in vernalization, Genes Dev, vol.27, pp.1845-1850, 2013.
, Identification of the endodermal vacuole as the iron storage compartment in the Arabidopsis embryo, Plant Physiol, vol.151, pp.1329-1338, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00445498
, Plant cell nucleolus as a hot spot for iron, J Biol Chem, vol.286, pp.27863-27866, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00623165
, Integrative epigenomic mapping defines four main chromatin states in Arabidopsis, EMBO J, vol.30, pp.1928-1938, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00999846
, Identification of functional elements and regulatory circuits by Drosophila modENCODE, Science, vol.330, pp.1787-1797, 2010.
, Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants, Plant Mol Biol, vol.66, pp.637-646, 2008.
, DNA dynamics during early double-strand break processing revealed by non-intrusive imaging of living cells, PLoS Genet, vol.10, p.1004187, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01117870
, A plant snoRNP complex containing snoRNAs, fibrillarin, and nucleolin-like proteins is competent for both rRNA gene binding and pre-rRNA processing in vitro, Mol Cell Biol, vol.24, pp.7284-7297, 2004.
, Nuclear localization activity of phytochrome B, Plant J Cell Mol Biol, vol.10, pp.859-868, 1996.
, Identification of protein factors and U3 snoRNAs from a Brassica oleracea RNP complex involved in the processing of pre-rRNA, Plant J Cell Mol Biol, vol.61, pp.383-398, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00787658
, Pre-mRNA splicing: life at the centre of the central dogma, J Cell Sci, vol.117, pp.6261-6263, 2004.
, A steroid-inducible gene expression system for plant cells, Proc Natl Acad Sci U S A, vol.88, pp.10421-10425, 1991.
, Threading the barrel of the RNA exosome, Trends Biochem Sci, vol.38, pp.485-493, 2013.
, Ferritinopathy: diagnosis by muscle or nerve biopsy, with a note on other nuclear inclusion body diseases, Acta Neuropathol (Berl), vol.109, pp.109-114, 2005.
,
, Telomere repeat binding proteins are functional components of Arabidopsis telomeres and interact with telomerase, Plant J Cell Mol Biol, vol.77, pp.770-781
, Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness, Chromosoma, vol.121, pp.369-387, 2012.
, Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei, J Exp Bot, vol.66, pp.1687-1698, 2015.
, Heavy Metals Need Assistance: The Contribution of Nicotianamine to Metal Circulation Throughout the Plant and the Arabidopsis NAS Gene Family, Front Plant Sci, vol.2, p.69, 2011.
, PNAC: a protein nucleolar association classifier, BMC Genomics, vol.12, p.74, 2011.
, The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States, Plant Cell, vol.26, pp.2351-2366, 2014.
, Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus, Chromosoma, 2015.
, Three-dimensional folding and functional organization principles of the Drosophila genome, Cell, vol.148, pp.458-472, 2012.
, The nucleolus, Annu Rev Cell Dev Biol, vol.11, pp.93-121, 1995.
, Distinct 18S rRNA precursors are targets of the exosome complex, the exoribonuclease RRP6L2 and the terminal nucleotidyltransferase TRL in Arabidopsis thaliana, Plant J Cell Mol Biol, vol.83, pp.991-1004, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01208204
, snRNP protein expression enhances the formation of Cajal bodies containing p80-coilin and SMN, J Cell Sci, vol.114, pp.4407-4419, 2001.
, The ubiquitin 26S proteasome proteolytic pathway, Annu Rev Plant Biol, vol.55, pp.555-590, 2004.
, Nuclear speckles, Cold Spring Harb Perspect Biol, vol.3, 2011.
, The new cytogenetics: blurring the boundaries with molecular biology, Nat Rev Genet, vol.6, pp.782-792, 2005.
, Potential roles for ubiquitin and the proteasome during ribosome biogenesis, Mol Cell Biol, vol.26, pp.5131-5145, 2006.
, Functional ultrastructure of the plant nucleolus, Protoplasma, vol.251, pp.1285-1306, 2014.
, Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome, Cell, vol.152, pp.352-364, 2013.
, Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana, Cell Rep, vol.8, pp.2015-2030, 2014.
, Nuclear pore association confers optimal expression levels for an inducible yeast gene, Nature, vol.441, pp.774-778, 2006.
, Involvement of the plant nucleolus in virus and viroid infections: parallels with animal pathosystems, Adv Virus Res, vol.77, pp.119-158, 2010.
, Identification and characterization of nuclear pore complex components in Arabidopsis thaliana, Plant Cell, vol.22, pp.4084-4097, 2010.
, Building a plant: cell fate specification in the early Arabidopsis embryo, Chromosome Res Int J Mol Supramol Evol Asp Chromosome Biol, vol.22, pp.420-430, 2014.
, Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis, Plant J Cell Mol Biol, vol.50, pp.848-857, 2007.
, Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana, PLoS Genet, vol.5, p.1000638, 2009.
, Birth of a nucleolus: the evolution of nucleolar compartments, Trends Cell Biol, vol.15, pp.194-199, 2005.
, Nucleolar clustering of dispersed tRNA genes, Science, vol.302, pp.1399-1401, 2003.
, Novel endoribonucleases as central players in various pathways of eukaryotic RNA metabolism, RNA N Y N, vol.16, pp.1692-1724, 2010.
, Cell cycle-regulated trafficking of human telomerase to telomeres, Mol Biol Cell, vol.17, pp.955-965, 2006.
, Nucleolar dominance and ribosomal RNA gene silencing, Curr Opin Cell Biol, vol.22, pp.351-356, 2010.
, Photobodies in light signaling, Plant Physiol, vol.158, pp.52-60, 2012.
, High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli, Proc Natl Acad Sci U S A, vol.21, pp.583-590, 2010.
, ATM regulates the length of individual telomere tracts in Arabidopsis, Proc Natl Acad Sci U S A, vol.104, pp.18145-18150, 2007.
, Nucleolar changes in human phytohaemagglutinin-stimulated lymphocytes, Cell Tissue Res, vol.213, pp.351-360, 1980.
, Nucleolus organizer regions in human lymphocytes as studied with premature chromosome condensation, Hum Genet, vol.84, pp.244-248, 1990.
, Genome-wide analysis of local chromatin packing in Arabidopsis thaliana, Genome Res, vol.25, pp.246-256, 2015.
, Genomewide nonadditive gene regulation in Arabidopsis allotetraploids, Genetics, vol.172, pp.507-517, 2006.
, Silencing near tRNA genes requires nucleolar localization, J Biol Chem, vol.280, pp.8637-8639, 2005.
, The nucleolus and viral infection, Virol Sin, vol.25, pp.151-157, 2010.
, Combinatorial patterns of histone acetylations and methylations in the human genome, Nat Genet, vol.40, pp.897-903, 2008.
, Nascent ribosomes from HeLa cells, Proc Natl Acad Sci U S A, vol.58, pp.1984-1990, 1967.
, The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA, Wiley Interdiscip Rev RNA, vol.3, pp.397-414, 2012.
, Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus in transgenic Arabidopsis, J Cell Biol, vol.145, pp.437-445, 1999.
, Structure-function relationships during transgenic telomerase expression in Arabidopsis, Physiol Plant, vol.149, pp.114-126, 2013.
, , 2014.
, Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin, EMBO J, vol.19, pp.6870-6881, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00023725
, Solution structure of the two N-terminal RNAbinding domains of nucleolin and NMR study of the interaction with its RNA target, J Mol Biol, vol.303, pp.227-241, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00023726
, A Polycomb-based switch underlying quantitative epigenetic memory, Nature, vol.476, pp.105-108, 2011.
, A glucocorticoid-mediated transcriptional induction system in transgenic plants, Plant J Cell Mol Biol, vol.11, pp.605-612, 1997.
, Nucleolus-associated telomere clustering and pairing precede meiotic chromosome synapsis in Arabidopsis thaliana, J Cell Sci, vol.114, pp.4207-4217, 2001.
, Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA, Mol Cell, vol.45, pp.147-157, 2012.
, The nucleolar detention pathway: A cellular strategy for regulating molecular networks, Cell Cycle Georget Tex, vol.11, pp.2059-2062, 2012.
, Changes of telomere length cause reciprocal changes in the lifespan of mother cells in Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, vol.94, pp.9768-9772, 1997.
, Bacterial chromosome organization and segregation, Annu Rev Cell Dev Biol, vol.31, pp.171-199, 2015.
,
, Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila, Cell, vol.144, pp.214-226
, Hi-C: a comprehensive technique to capture the conformation of genomes, Methods San Diego Calif, vol.58, pp.268-276, 2012.
, Heterochromatin dynamics during developmental transitions in Arabidopsis -a focus on ribosomal DNA loci, Gene, vol.526, pp.39-45, 2013.
,
, High-resolution statistical mapping reveals gene territories in live yeast, Nat Methods, vol.5, pp.1031-1037
, Environmental perception and epigenetic memory: mechanistic insight through FLC, Plant J Cell Mol Biol, vol.83, pp.133-148, 2015.
, Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance, 2015.
, Genome architecture: domain organization of interphase chromosomes, Cell, vol.152, pp.1270-1284, 2013.
, Heterosis. Plant Cell, vol.22, pp.2105-2112, 2010.
, A two-step process for epigenetic inheritance in Arabidopsis, Mol Cell, vol.54, pp.30-42, 2014.
, The multifunctional nucleolus, Nat Rev Mol Cell Biol, vol.8, pp.574-585, 2007.
, Inducible gene expression systems for plants, Methods Mol Biol Clifton NJ, vol.655, pp.65-75, 2010.
, The movement of coiled bodies visualized in living plant cells by the green fluorescent protein, Mol Biol Cell, vol.10, pp.2297-2307, 1999.
, The nucleolus under stress, Mol Cell, vol.40, pp.216-227, 2010.
, Light signaling controls nuclear architecture reorganization during seedling establishment, Proc Natl Acad Sci U S A, vol.112, pp.2836-2844, 2015.
, Recognition of pre-formed and flexible elements of an RNA stem-loop by nucleolin, J Mol Biol, vol.309, pp.763-775, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00023732
, Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes, Proc Natl Acad Sci U S A, vol.108, pp.4334-4339, 2011.
, High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation, Plant Cell, vol.23, pp.873-894, 2011.
, Accounting for technical noise in single-cell RNA-seq experiments, Nat Methods, vol.10, pp.1093-1095, 2013.
, Ferritins and iron storage in plants, Biochim Biophys Acta, vol.1800, pp.806-814, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00507415
, ABSENCE OF RIBOSOMAL RNA SYNTHESIS IN THE ANUCLEOLATE MUTANT OF XENOPUS LAEVIS, Proc Natl Acad Sci, vol.51, pp.139-146, 1964.
, To be or not to be in the nucleolus, Nat Cell Biol, vol.2, pp.107-112, 2000.
, Depletion of the yeast nuclear exosome subunit Rrp6 results in accumulation of polyadenylated RNAs in a discrete domain within the nucleolus, Mol Cell Biol, vol.27, pp.4157-4165, 2007.
, Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization, Cell, vol.117, pp.427-439, 2004.
, Alu elementcontaining RNAs maintain nucleolar structure and function, EMBO J, vol.34, pp.2758-2774, 2015.
, Chromosomespecific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis, Genes Dev, vol.30, pp.177-190, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01313216
, Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system, Cell, vol.155, pp.1479-1491, 2013.
, Arabidopsis HEMERA/pTAC12 initiates photomorphogenesis by phytochromes, Cell, vol.141, pp.1230-1240, 2010.
, Characterization of the requirements for localization of phytochrome B to nuclear bodies, Proc Natl Acad Sci, vol.100, pp.14493-14498, 2003.
, Genomic and epigenetic insights into the molecular bases of heterosis, Nat Rev Genet, vol.14, pp.471-482, 2013.
, Molecular mechanisms of polyploidy and hybrid vigor, Trends Plant Sci, vol.15, pp.57-71, 2010.
, Real-time dynamics of RNA polymerase II clustering in live human cells, Science, vol.341, pp.664-667, 2013.
, A distant coilin homologue is required for the formation of cajal bodies in Arabidopsis, Mol Biol Cell, vol.17, pp.2942-2951, 2006.
, Characterization of a ribonuclease III-like protein required for cleavage of the pre-rRNA in the 3'ETS in Arabidopsis, Nucleic Acids Res, vol.36, pp.1163-1175, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02121738
, The organization of replication and transcription, Science, vol.284, pp.1790-1795, 1999.
, RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4, Plant J Cell Mol Biol, vol.9, pp.259-272, 1996.
,
, Metal movement within the plant: contribution of nicotianamine and yellow stripe, Ann Bot, vol.103, pp.1-11
, Capturing chromosome conformation, Science, vol.295, pp.1306-1311, 2002.
, Nucleolar activation and vacuolation in embryo radicle cells during early germination, J Cell Sci, vol.76, pp.67-83, 1985.
, Controlling gene expression in response to stress, Nat Rev Genet, vol.12, pp.833-845, 2011.
, Ultrastructural cytochemistry of the mammalian cell nucleolus, J Histochem Cytochem Off J Histochem Soc, vol.38, pp.1237-1256, 1990.
, Connecting the transcription site to the nuclear pore: a multi-tether process that regulates gene expression, J Cell Sci, vol.123, pp.1989-1999, 2010.
, Cell identity mediates the response of Arabidopsis roots to abiotic stress, Science, vol.320, pp.942-945, 2008.
, LITTLE NUCLEI genes affecting nuclear morphology in Arabidopsis thaliana, Plant Cell, vol.19, pp.2793-2803, 2007.
, A duplicated NUCLEOLIN gene with antagonistic activity is required for chromatin organization of silent 45S rDNA in Arabidopsis, Plant Cell, vol.26, pp.1330-1344, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02116071
, Nucleolin: dual roles in rDNA chromatin transcription, Gene, vol.556, pp.7-12, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02116040
, Chromatin dynamics of plant telomeres and ribosomal genes, Plant J Cell Mol Biol, vol.83, pp.18-37, 2015.
, Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation, Genes Dev, vol.24, pp.1119-1132, 2010.
, Quantification of cell identity from singlecell gene expression profiles, Genome Biol, vol.16, p.9, 2015.
, Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development, Dev Camb Engl, vol.133, pp.4163-4172, 2006.
, Nucleation by rRNA Dictates the Precision of Nucleolus Assembly, Curr Biol CB, vol.26, pp.277-285, 2016.
, High resolution autoradiography studies on chromatin functions, pp.3-53, 1978.
, Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis, Mol Biol Cell, vol.15, pp.2664-2673, 2004.
, Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants, Curr Biol CB, vol.17, pp.818-823, 2007.
, Light-regulated gene repositioning in Arabidopsis, Nat Commun, vol.5, p.3027, 2014.
, Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Casinduced gene modifications in Arabidopsis, Proc Natl Acad Sci U S A, vol.111, pp.4632-4637, 2014.
, AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins, Mol Cell Proteomics MCP, vol.9, pp.1063-1084, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00470319
, Systematic protein location mapping reveals five principal chromatin types in Drosophila cells, Cell, vol.143, pp.212-224, 2010.
, Considering transposable element diversification in de novo annotation approaches, PloS One, vol.6, p.16526, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00568705
, 1781. traité sur le venin de la vipère, avec des observations sur la structure primitive du corps animale
, Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate, Proc Natl Acad Sci U S A, vol.99, pp.14584-14589, 2002.
, The centennial of the Cajal body, Nat Rev Mol Cell Biol, vol.4, pp.975-980, 2003.
, Nucleolar factors direct the 2'-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA, Mol Cell Biol, vol.19, pp.6906-6917, 1999.
, The hierarchy of the 3D genome, Mol Cell, vol.49, pp.773-782, 2013.
, Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing, Curr Opin Cell Biol, vol.17, pp.281-286, 2005.
, Nuclear envelope dynamics during plant cell division suggest common mechanisms between kingdoms, Biochem J, vol.435, pp.661-667, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00586467
, Plant SUN domain proteins: components of putative plant LINC complexes?, Plant Signal Behav, vol.5, pp.154-156, 2010.
, Iron in seeds -loading pathways and subcellular localization, Front Plant Sci, vol.4, p.535, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01048736
, Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division, Genes Dev, vol.28, pp.220-230, 2014.
, Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture, Genome Biol, vol.14, p.129, 2013.
, Epigenetic control of RNA polymerase I transcription in mammalian cells, Biochim Biophys Acta, vol.1829, pp.393-404, 2013.
, Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions, Nature, vol.453, pp.948-951, 2008.
, Spatial reorganization of telomeres in long-lived quiescent cells, Genome Biol, vol.16, p.206, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01206018
, Localization of modified nucleotides in Schizosaccharomyces pombe spliceosomal small nuclear RNAs: modified nucleotides are clustered in functionally important regions, RNA N Y N, vol.2, pp.909-918, 1996.
, Isolation of nucleoli, Curr Protoc Cell Biol Editor Board Juan Bonifacino Al Chapter, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00709427
, Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes, Genes Dev, vol.22, pp.2204-2214, 2008.
, CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing, Nat Struct Mol Biol, vol.20, pp.1358-1366, 2013.
, Molecular analysis of telomere fusions in Arabidopsis: multiple pathways for chromosome end-joining, EMBO J, vol.23, pp.2304-2313, 2004.
, The ins and outs of gene regulation and chromosome territory organisation, Curr Opin Cell Biol, vol.19, pp.311-316, 2007.
, Nukleolen und Chromosomen in der Gattung Vicia, Planta, vol.15, pp.495-505, 1931.
, Assembly and disassembly of the nucleolus during the cell cycle, Nucl Austin Tex, vol.2, pp.189-194, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00666117
, Emerging concepts of nucleolar assembly, J Cell Sci, vol.115, pp.2265-2270, 2002.
, RNA viruses: hijacking the dynamic nucleolus, Nat Rev Microbiol, vol.5, pp.119-127, 2007.
, Nucleolar proteomics and viral infection, Proteomics, vol.10, pp.4077-4086, 2010.
, The many pathways of RNA degradation, Cell, vol.136, pp.763-776, 2009.
, Three-dimensional reconstructions of nucleolus-organizing regions in, Biol Cell Auspices Eur Cell Biol Organ, vol.66, pp.225-233, 1989.
, Abundance of ribosomal RNA gene copies maintains genome integrity, Science, vol.327, pp.693-696, 2010.
, Control of transposable elements in Arabidopsis thaliana, Chromosome Res Int J Mol Supramol Evol Asp Chromosome Biol, vol.22, pp.217-223, 2014.
, Environmental cues induce a long noncoding RNA-dependent remodeling of the nucleolus, Mol Biol Cell, vol.24, pp.2943-2953, 2013.
, ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing, Nat Struct Mol Biol, vol.16, pp.763-768, 2009.
, Cell cycle-dependent recruitment of telomerase RNA and Cajal bodies to human telomeres, Mol Biol Cell, vol.17, pp.944-954, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00021198
, Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice, Nucleic Acids Res, vol.41, p.188, 2013.
, Telomeres, the nucleolus and aging, Curr Opin Cell Biol, vol.10, pp.332-338, 1998.
, Dyskerin is a component of the Arabidopsis telomerase RNP required for telomere maintenance, Mol Cell Biol, vol.28, pp.2332-2341, 2008.
, Comprehensive analysis of the chromatin landscape in Drosophila melanogaster, Nature, vol.471, pp.480-485, 2011.
,
, Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus, Plant Cell, vol.21, pp.2045-2057
, Interaction of a plant virus-encoded protein with the major nucleolar protein fibrillarin is required for systemic virus infection, Proc Natl Acad Sci U S A, vol.104, pp.11115-11120, 2007.
, Cajal bodies and the nucleolus are required for a plant virus systemic infection, EMBO J, vol.26, pp.2169-2179, 2007.
, Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells, Cell, vol.163, pp.134-147, 2015.
, Single-cell dynamics of genome-nuclear lamina interactions, Cell, vol.153, pp.178-192, 2013.
, Chromatin modifications and their function, Cell, vol.128, pp.693-705, 2007.
, Degradation of a polyadenylated rRNA maturation by-product involves one of the three RRP6-like proteins in Arabidopsis thaliana, Mol Cell Biol, vol.28, pp.3038-3044, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00309545
, The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana, PLoS Genet, vol.10, p.1004564, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01067729
, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-359, 2012.
, Catalytically active telomerase holoenzyme is assembled in the dense fibrillar component of the nucleolus during S phase, Histochem Cell Biol, vol.141, pp.137-152, 2014.
, Arabidopsis CBF5 interacts with the H/ACA snoRNP assembly factor NAF1, Plant Mol Biol, vol.65, pp.615-626, 2007.
, An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana, Cell, vol.126, pp.93-106, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00164266
, Widespread rearrangement of 3D chromatin organization underlies polycombmediated stress-induced silencing, Mol Cell, vol.58, pp.216-231, 2015.
, Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model, Mol Biol Cell, vol.25, pp.1366-1373, 2014.
, Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation, Nat Rev Genet, vol.9, pp.583-593, 2008.
, Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets, Biol Direct, vol.8, p.6, 2013.
, DNA binding within the nucleosome core, Curr Opin Struct Biol, vol.8, pp.33-40, 1998.
, Recruitment of RPL11 at promoter sites of p53-regulated genes upon nucleolar stress through NEDD8 and in an Mdm2-dependent manner, Oncogene, vol.31, pp.3060-3071, 2012.
, UBF-binding site arrays form pseudoNORs and sequester the RNA polymerase I transcription machinery, Genes Dev, vol.19, pp.50-64, 2005.
, Biogenesis and function of nuclear bodies, Trends Genet TIG, vol.27, pp.295-306, 2011.
, Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis, Plant Cell, vol.15, pp.2929-2939, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01917210
, RNA-mediated chromatin-based silencing in plants, Curr Opin Cell Biol, vol.21, pp.367-376, 2009.
, The relationship of a particular chromosomal element to the development of the nucleoli in Zea mays, Zeit Zellforsch Mik Anat, vol.21, pp.294-328, 1934.
, The epigenetics of rRNA genes: from molecular to chromosome biology, Annu Rev Cell Dev Biol, vol.24, pp.131-157, 2008.
, Building silent compartments at the nuclear periphery: a recurrent theme, Curr Opin Genet Dev, vol.23, pp.96-103, 2013.
, Gateway-compatible tissue-specific vectors for plant transformation, BMC Res Notes, vol.8, p.63, 2015.
, Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation, Mol Cell Proteomics MCP, vol.10, 2011.
, Transactivated and chemically inducible gene expression in plants, Plant J Cell Mol Biol, vol.45, pp.651-683, 2006.
, Nucleolar Ultrastructure in Vertebrates, The Nucleolus, pp.10-20
, Dysfunction of chromatin assembly factor 1 induces shortening of telomeres and loss of 45S rDNA in Arabidopsis thaliana, Plant Cell, vol.22, pp.2768-2780, 2010.
,
, Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis, Proc Natl Acad Sci U S A, vol.106, pp.18843-18848
, Initial genomics of the human nucleolus, PLoS Genet, vol.6, p.1000889, 2010.
, Genome organization in and around the nucleolus, Trends Genet TIG, vol.27, pp.149-156, 2011.
, Localization of nucleolar phosphoproteins B23 and C23 during mitosis, Exp Cell Res, vol.146, pp.139-149, 1983.
, Nucleologenesis: composition and fate of prenucleolar bodies, Chromosoma, vol.92, pp.330-336, 1985.
, The nucleoplasmin homolog NLP mediates centromere clustering and anchoring to the nucleolus, Mol Cell, vol.50, pp.236-249, 2013.
, Transcription factories: genome organization and gene regulation, Chem Rev, vol.113, pp.8683-8705, 2013.
, Ribosomal DNA deletions modulate genome-wide gene expression: "rDNA-sensitive" genes and natural variation, PLoS Genet, vol.7, p.1001376, 2011.
, Ribosomal DNA contributes to global chromatin regulation, Proc Natl Acad Sci U S A, vol.106, pp.17829-17834, 2009.
, Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth, J Exp Bot, vol.65, pp.6057-6067, 2014.
, Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions, Mol Biol Cell, vol.16, pp.260-269, 2005.
, tRNA biology charges to the front, Genes Dev, vol.24, pp.1832-1860, 2010.
, Epigenetic regulation in plants, Cold Spring Harb Perspect Biol, vol.6, p.19315, 2014.
, Recent advances in X-chromosome inactivation research, Curr Opin Cell Biol, vol.24, pp.825-832, 2012.
, Three-dimensional genome architecture: players and mechanisms, Nat Rev Mol Cell Biol, vol.16, pp.245-257, 2015.
, The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center, Cell, vol.126, pp.79-92, 2006.
, siRNA and miRNA processing: new functions for Cajal bodies, Curr Opin Genet Dev, vol.18, pp.197-203, 2008.
, Intersection of small RNA pathways in Arabidopsis thaliana sub-nuclear domains, PloS One, vol.8, p.65652, 2013.
, Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana, PLoS Genet, vol.6, p.1001225, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00787644
, Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis, Genes Dev, vol.26, pp.945-957, 2012.
, Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states, Genes Dev, vol.27, pp.1545-1550, 2013.
, Arabidopsis Histone Lysine Methyltransferases, Adv Bot Res, vol.53, pp.1-22, 2010.
, Characterization of AtNUC-L1 reveals a central role of nucleolin in nucleolus organization and silencing of AtNUC-L2 gene in Arabidopsis, Mol Biol Cell, vol.18, pp.369-379, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00164253
, Mod5 protein binds to tRNA gene complexes and affects local transcriptional silencing, Proc Natl Acad Sci U S A, vol.110, pp.3081-3089, 2013.
, Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins, Mol Cell, vol.32, pp.673-684, 2008.
, rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch, Biochim Biophys Acta, vol.1769, pp.383-392, 2007.
, Recruitment of factors linking transcription and processing of prerRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells, Genes Dev, vol.21, pp.2041-2054, 2007.
, Study of the localization of iron, ferritin, and hemosiderin in Alzheimer's disease hippocampus by analytical microscopy at the subcellular level, J Struct Biol, vol.153, pp.42-54, 2006.
, Control of nuclear and nucleolar localization of nuclear inclusion protein a of picorna-like Potato virus A in Nicotiana species, Plant Cell, vol.21, pp.2485-2502, 2009.
, New insights into nucleolar architecture and activity, Int Rev Cytol, vol.255, pp.177-235, 2006.
, The nucleolar structure in plant cells, Revis Sobre Biol Cel RBC, vol.7, pp.1-154, 1986.
, LOCALIZATION OF DNA COMPLEMENTARY TO RIBOSOMAL RNA IN THE NUCLEOLUS ORGANIZER REGION OF DROSOPHILA MELANOGASTER, Proc Natl Acad Sci U S A, vol.53, pp.737-745, 1965.
, Physical clustering of FLC alleles during Polycomb-mediated epigenetic silencing in vernalization, Genes Dev, vol.27, pp.1845-1850, 2013.
, Identification of the endodermal vacuole as the iron storage compartment in the Arabidopsis embryo, Plant Physiol, vol.151, pp.1329-1338, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00445498
, Plant cell nucleolus as a hot spot for iron, J Biol Chem, vol.286, pp.27863-27866, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00623165
, Integrative epigenomic mapping defines four main chromatin states in Arabidopsis, EMBO J, vol.30, pp.1928-1938, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00999846
, Identification of functional elements and regulatory circuits by Drosophila modENCODE, Science, vol.330, pp.1787-1797, 2010.
, Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants, Plant Mol Biol, vol.66, pp.637-646, 2008.
, DNA dynamics during early double-strand break processing revealed by non-intrusive imaging of living cells, PLoS Genet, vol.10, p.1004187, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01117870
, A plant snoRNP complex containing snoRNAs, fibrillarin, and nucleolin-like proteins is competent for both rRNA gene binding and pre-rRNA processing in vitro, Mol Cell Biol, vol.24, pp.7284-7297, 2004.
, Nuclear localization activity of phytochrome B, Plant J Cell Mol Biol, vol.10, pp.859-868, 1996.
, Identification of protein factors and U3 snoRNAs from a Brassica oleracea RNP complex involved in the processing of pre-rRNA, Plant J Cell Mol Biol, vol.61, pp.383-398, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00787658
, Pre-mRNA splicing: life at the centre of the central dogma, J Cell Sci, vol.117, pp.6261-6263, 2004.
, A steroid-inducible gene expression system for plant cells, Proc Natl Acad Sci U S A, vol.88, pp.10421-10425, 1991.
, Threading the barrel of the RNA exosome, Trends Biochem Sci, vol.38, pp.485-493, 2013.
, Ferritinopathy: diagnosis by muscle or nerve biopsy, with a note on other nuclear inclusion body diseases, Acta Neuropathol (Berl), vol.109, pp.109-114, 2005.
,
, Telomere repeat binding proteins are functional components of Arabidopsis telomeres and interact with telomerase, Plant J Cell Mol Biol, vol.77, pp.770-781
, Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness, Chromosoma, vol.121, pp.369-387, 2012.
, Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei, J Exp Bot, vol.66, pp.1687-1698, 2015.
, Heavy Metals Need Assistance: The Contribution of Nicotianamine to Metal Circulation Throughout the Plant and the Arabidopsis NAS Gene Family, Front Plant Sci, vol.2, p.69, 2011.
, PNAC: a protein nucleolar association classifier, BMC Genomics, vol.12, p.74, 2011.
, The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States, Plant Cell, vol.26, pp.2351-2366, 2014.
, Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus, Chromosoma, 2015.
, Three-dimensional folding and functional organization principles of the Drosophila genome, Cell, vol.148, pp.458-472, 2012.
, The nucleolus, Annu Rev Cell Dev Biol, vol.11, pp.93-121, 1995.
, Distinct 18S rRNA precursors are targets of the exosome complex, the exoribonuclease RRP6L2 and the terminal nucleotidyltransferase TRL in Arabidopsis thaliana, Plant J Cell Mol Biol, vol.83, pp.991-1004, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01208204
, snRNP protein expression enhances the formation of Cajal bodies containing p80-coilin and SMN, J Cell Sci, vol.114, pp.4407-4419, 2001.
, The ubiquitin 26S proteasome proteolytic pathway, Annu Rev Plant Biol, vol.55, pp.555-590, 2004.
, Nuclear speckles, Cold Spring Harb Perspect Biol, vol.3, p.646, 2011.
, The new cytogenetics: blurring the boundaries with molecular biology, Nat Rev Genet, vol.6, pp.782-792, 2005.
, Potential roles for ubiquitin and the proteasome during ribosome biogenesis, Mol Cell Biol, vol.26, pp.5131-5145, 2006.
, Functional ultrastructure of the plant nucleolus, Protoplasma, vol.251, pp.1285-1306, 2014.
, Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome, Cell, vol.152, pp.352-364, 2013.
, Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana, pathways of eukaryotic RNA metabolism. RNA N Y N, vol.8, pp.1692-1724, 2014.
, Cell cycle-regulated trafficking of human telomerase to telomeres, Mol Biol Cell, vol.17, pp.955-965, 2006.
, Nucleolar dominance and ribosomal RNA gene silencing, Curr Opin Cell Biol, vol.22, pp.351-356, 2010.
, Photobodies in light signaling, Plant Physiol, vol.158, pp.52-60, 2012.
, High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli, Mol Biol Cell, vol.21, pp.3735-3748, 2010.
, Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation, Proc Natl Acad Sci U S A, vol.108, pp.20219-20224, 2011.
, Shedding light on large-scale chromatin reorganization in Arabidopsis thaliana, Mol Plant, vol.5, pp.583-590, 2012.
, ATM regulates the length of individual telomere tracts in Arabidopsis, Proc Natl Acad Sci U S A, vol.104, pp.18145-18150, 2007.
, Nucleolar changes in human phytohaemagglutinin-stimulated lymphocytes, Cell Tissue Res, vol.213, pp.351-360, 1980.
, Nucleolus organizer regions in human lymphocytes as studied with premature chromosome condensation, Hum Genet, vol.84, pp.244-248, 1990.
, Genome-wide analysis of local chromatin packing in Arabidopsis thaliana, Genome Res, vol.25, pp.246-256, 2015.
, Genomewide nonadditive gene regulation in Arabidopsis allotetraploids, Genetics, vol.172, pp.507-517, 2006.
, Silencing near tRNA genes requires nucleolar localization, J Biol Chem, vol.280, pp.8637-8639, 2005.
, The nucleolus and viral infection, Virol Sin, vol.25, pp.151-157, 2010.
, Combinatorial patterns of histone acetylations and methylations in the human genome, Nat Genet, vol.40, pp.897-903, 2008.
, Nascent ribosomes from HeLa cells, Proc Natl Acad Sci U S A, vol.58, pp.1984-1990, 1967.
, The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA, Wiley Interdiscip Rev RNA, vol.3, pp.397-414, 2012.
, Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus in transgenic Arabidopsis, J Cell Biol, vol.145, pp.437-445, 1999.
, Structure-function relationships during transgenic telomerase expression in Arabidopsis, Physiol Plant, vol.149, pp.114-126, 2013.
, Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy, Proc Natl Acad Sci U S A, vol.111, pp.681-686, 2014.
, The region of interest was amplified using primers described in Pontvianne et al. (2010a); resulting PCR products were cloned into pGEM-T-Easy (Promega) and sequenced using an ABI3730 machine. Sequenced clones were analyzed using CyMATE (Hetzl et al. 2007) and graphed using a custom Perl script and Microsoft Excel, BamHI, 2 mg of DNA was bisulfite-treated using an Epitect Bisulfite kit (Qiagen)
, anti-Pol I, or anti-H3K27me1 antibodies as described, DNA was amplified using Platinum Taq Polymerase (Invitrogen), 2009.
, Internal Reference dye (Sigma), and an Applied Biosystems model 7500 thermocycler. Results were analyzed using the comparative CT method (Livak and Schmittgen 2001) relative to input. For the ChIP coupled with deep sequencing (ChIP-seq) analyses shown in Supplemental Figure S4, genomic sequencing reads were mapped to a previously described rDNA sequence, Green I (Invitrogen), 2008.
, DNA-FISH analyses were performed using nuclei from leaves of 4-wk-old plants, as previously described, 2007.
, 2 mM NaEDTA, 0.5 mM spermine, 80 mM KCl, 20 mM NaCl, 0.1% Triton X-100). The lysate was filtered through a 40-mm cell strainer (BD Falcon), and 12 mL of sorting buffer (100 mM Tris-HCl at pH 7.5, 50 mM KCl, 2 mM MgCl2, 0.05% Tweenseries (70%, 90%, and 100% for 2 min each) prior to hybridization in formamide buffer (50% formamide, 23 SSC, 50 mM sodium phosphate at pH 7.0, 10% dextran sulphate) with 5S or 45S rRNA gene probes labeled with biotin-16-UTP (Roche) or digoxigenin-11-UTP (Roche), 4% formaldehyde in Tris buffer (10 mM Tris-HCL at pH 7.5, 10 mM EDTA, 100 mM NaCl), then chopped as finely as possible with a razor blade in 0.5 mL of LB01 buffer (15 mM Tris-HCl at pH 7.5, p.100
, Vector Laboratories) and avidin-Texas Red (1:500) were used for the detection of the biotin-labeled probe, p.125
, Roche) followed by rabbit anti-mouse fluorescein isothiocyanate (FITC, p.500
, Molecular Probes) were used for the detection of the digoxigenin-labeled probe. Nuclei were then counterstained with DAPI. An Applied Precision DeltaVision personal DV microscope and SoftWorx and Imaris imaging software were used to analyze the data, Sigma) and Alexa 488-conjugated goat anti-rabbit, vol.2, pp.204-299, 2011.
, HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA, EMBO J, vol.21, pp.6832-6841, 2002.
, The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes, Nucleic Acids Res, vol.29, pp.4319-4333, 2001.
, Determinants and dynamics of genome accessibility, Nat Rev Genet, vol.12, pp.554-564, 2011.
, Epigenetic silencing of RNA polymerase I transcription: A role for DNA methylation and histone modification in nucleolar dominance, Genes Dev, vol.11, pp.2124-2136, 1997.
, Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids, Proc Natl Acad Sci, vol.95, pp.14891-14896, 1998.
, Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature, vol.452, pp.215-219, 2008.
, RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4, Plant J, vol.9, pp.259-272, 1996.
, HKMTs and rRNA gene dosage control GENES & DEVELOPMENT 955
, Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution, vol.9, pp.273-282, 1996.
, Erasure of histone acetylation by Arabidopsis HDA6 mediates largescale gene silencing in nucleolar dominance, Genes Dev, vol.20, pp.1283-1293, 2006.
, Gateway-compatible vectors for plant functional genomics and proteomics, Plant J, vol.45, pp.616-629, 2006.
, Mechanisms of HDA6-mediated rRNA gene silencing: Suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation, Genes Dev, vol.24, pp.1119-1132, 2010.
, Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase, Plant Cell, vol.18, pp.1166-1176, 2006.
, H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases, Mol Cell Biol, vol.25, pp.10507-10515, 2005.
, A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands, Proc Natl Acad Sci, vol.89, pp.1827-1831, 1992.
, Structure and functions of nucleolin, J Cell Sci, vol.112, pp.761-772, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00023721
, Crosstalk in gene expression: Coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing, Curr Opin Cell Biol, vol.17, pp.281-286, 2005.
, Different epigenetic layers engage in complex crosstalk to define the epigenetic state of mammalian rRNA genes, Hum Mol Genet, vol.16, pp.21-27, 2007.
, Epigenetic silencing of RNA polymerase I transcription, Nat Rev Mol Cell Biol, vol.4, pp.641-649, 2003.
, Quantitative determination of rDNA transcription units in vertebrate cells, Exp Cell Res, vol.193, pp.78-86, 1991.
, CyMATE: A new tool for methylation analysis of plant genomic DNA after bisulphite sequencing, Plant J, vol.51, pp.526-536, 2007.
, Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase, Nature, vol.416, pp.556-560, 2002.
, ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing, Nat Struct Mol Biol, vol.16, pp.763-768, 2009.
, Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases, Nature, vol.466, pp.987-991, 2010.
, Histone modifications in Arabidopsishigh methylation of H3 lysine 9 is dispensable for constitutive heterochromatin, Plant J, vol.33, pp.471-480, 2003.
, Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation, Curr Biol, vol.12, pp.1360-1367, 2002.
, The SRA methyl-cytosine-binding domain links DNA and histone methylation, Curr Biol, vol.17, pp.379-384, 2007.
, SRA-domain proteins required for DRM2-mediated de novo DNA methylation, PLoS Genet, vol.4, p.1000280, 2008.
, Driving ribosome assembly, Biochim Biophys Acta, vol.1803, pp.673-683, 2010.
, C2H2 zinc finger-SET histone methyltransferase is a plant-specific chromatin modifier, Dev Biol, vol.303, pp.259-269, 2007.
, The many faces of histone lysine methylation, Curr Opin Cell Biol, vol.14, pp.286-298, 2002.
, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, p.25, 2009.
, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat Rev Genet, vol.11, pp.204-220, 2010.
, Transgene-induced RNA interference: A strategy for overcoming gene redundancy in polyploids to generate loss-of-function mutations, Plant J, vol.36, pp.114-121, 2003.
, Chromatin turn ons and turn offs of ribosomal RNA genes, Cell Cycle, vol.3, pp.880-883, 2004.
, A concerted DNA methylation/ histone methylation switch regulates rRNA gene dosage control and nucleolar dominance, Mol Cell, vol.13, pp.599-609, 2004.
, Restricted chromosomal silencing in nucleolar dominance, Proc Natl Acad Sci, vol.98, pp.14536-14540, 2001.
, Analysis of relative gene expression data using real-time quantitative PCR and the 2 ÀD D C(T) method, Methods, vol.25, pp.402-408, 2001.
, Repeated genes in eukaryotes, Annu Rev Biochem, vol.49, pp.727-764, 1980.
, An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation, EMBO J, vol.21, pp.6842-6852, 2002.
, Chromatin: Linking structure and function in the nucleolus, Chromosoma, vol.118, pp.11-23, 2009.
, Nucleolar dominance: A model for rRNA gene silencing, Genes Dev, vol.20, pp.1207-1214, 2006.
, The epigenetics of rRNA genes: From molecular to chromosome biology, Annu Rev Cell Dev Biol, vol.24, pp.131-157, 2008.
, Nucleolin: A multiFACeTed protein, Trends Cell Biol, vol.17, pp.80-86, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00337685
, A housekeeper with power of attorney: The rRNA genes in ribosome biogenesis, Cell Mol Life Sci, vol.64, pp.29-49, 2007.
, Gene silencing in plants using artificial microRNAs and other small RNAs, Plant J, vol.53, pp.674-690, 2008.
, The epigenetics of nucleolar dominance, Trends Genet, vol.16, pp.495-500, 2000.
, Postembryonic establishment of megabase-scale gene silencing in nucleolar ONE 2: e1157, 2007.
, Characterization of AtNUC-L1 reveals a central role of nucleolin in nucleolus organization and silencing of AtNUC-L2 gene in Arabidopsis, Mol Biol Cell, vol.18, pp.369-379, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00164253
, Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana, PLoS Genet, vol.6, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00787644
, Arabidopsis histone lysine methyltransferases, Adv Bot Res, vol.53, pp.1-22, 2010.
, Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins, Mol Cell, vol.32, pp.673-684, 2008.
, A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo, Genes Dev, vol.25, pp.137-152, 2011.
, Structure and function of the nucleolus in the spotlight, Curr Opin Cell Biol, vol.18, pp.325-334, 2006.
, Regulation of chromatin structure by site-specific histone H3 methyltransferases, Nature, vol.406, pp.593-599, 2000.
, Polymerase I transcription. InRegulation of transcription in plants, Grasser), vol.29, pp.162-183, 2007.
, Highly specific gene silencing by artificial microRNAs in Arabidopsis, Plant Cell, vol.18, pp.1121-1133, 2006.
, The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9, Nucleic Acids Res, vol.34, pp.5461-5470, 2006.
, Nucleolar dominance and ribosomal RNA gene silencing, Curr Opin Cell Biol, vol.22, pp.351-356, 2010.
, The SUVR4 histone lysine methyltransferase binds ubiquitin and converts H3K9me1 to H3K9me3 on transposon chromatin in Arabidopsis, PLoS Genet, vol.7, pp.635-648, 2008.
, HKMTs and rRNA gene dosage control GENES & DEVELOPMENT 957
, , 2016.
, Access the most recent version at doi, vol.26, pp.945-957, 2012.
, Genes Dev
,
, Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana, This article cites 60 articles, 18 of which can be accessed free at: References Barneche F, Steinmetz F, Echeverria M, vol.275, pp.27212-27220, 2000.
, Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci, J Cell Sci, vol.115, pp.2839-2846, 2002.
, RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4, Plant J, vol.9, pp.259-272, 1996.
, Use of RFLPs larger than 100 kbp to map the position and internal organization of the nucleolus organizer region on chromosome 2 in Arabidopsis thaliana, Plant J, vol.7, pp.273-286, 1995.
, Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance, Genes Dev, vol.20, pp.1283-1293, 2006.
, Mechanisms of HDA6-mediated rRNA gene silencing: Suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNAdirected cytosine methylation, Genes Dev, vol.24, pp.1119-1132, 2010.
, 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, Mol Cell Biol, vol.23, pp.1558-1568, 2003.
, Visualization of nucleolar organizer regions in mammalian chromosomes using silver staining, vol.53, pp.37-50, 1975.
, Epigenetic control of RNA polymerase I transcription in mammalian cells, Biochim Biophys Acta, vol.1829, pp.393-404, 2013.
, Dysregulation of RNA polymerase I transcription during disease, Biochim Biophys Acta, vol.1829, pp.342-360, 2013.
, CyMATE: A new tool for methylation analysis of plant genomic DNA after bisulphite sequencing, Plant J, vol.51, pp.526-536, 2007.
, Driving ribosome assembly, Biochim Biophys Acta, vol.1803, pp.673-683, 2010.
, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat Rev Genet, vol.11, pp.204-220, 2010.
, A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance, Mol Cell, vol.13, pp.599-609, 2004.
, The epigenetics of rRNA genes: From molecular to chromosome biology, Annu Rev Cell Dev Biol, vol.24, pp.131-157, 2008.
, A housekeeper with power of attorney: The rRNA genes in ribosome biogenesis, Cell Mol Life Sci, vol.64, pp.29-49, 2007.
, Dysfunction of chromatin assembly factor 1 induces shortening of telomeres and loss of 45S rDNA in Arabidopsis thaliana, Plant Cell, vol.22, pp.2768-2780, 2010.
, Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis, Proc Natl Acad Sci, vol.100, pp.11418-11423, 2003.
, The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center, Cell, vol.126, pp.79-92, 2006.
, Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana, PLoS Genet, vol.6, p.1001225, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00787644
, Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis, Genes Dev, vol.26, pp.945-957, 2012.
, Pseudo-NORs: A novel model for studying nucleoli, Biochim Biophys Acta, vol.1783, pp.2116-2123, 2008.
, Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats, Plant Cell, vol.16, pp.1021-1034, 2004.
, The many faces of chromatin assembly factor 1, Trends Plant Sci, vol.12, pp.570-576, 2007.
, Identification of Ag-NOR proteins, markers of proliferation related to ribosomal gene activity, Exp Cell Res, vol.214, pp.465-472, 1994.
, RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase, EMBO J, vol.21, pp.4959-4968, 2002.
, Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription, Mol Cell, vol.8, pp.719-725, 2001.
, Nucleolar dominance and ribosomal RNA gene silencing, Curr Opin Cell Biol, vol.22, pp.351-356, 2010.
,
, , 2016.
, Access the most recent version at doi, vol.27, pp.1545-1550, 2013.
, Genes Dev
,
, This article cites 28 articles, 10 of which can be accessed free at