Eukaryotic gene regulation in three dimensions and its impact on genome evolution.

[1]  D. Jackson,et al.  Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III , 1999, The EMBO journal.

[2]  M. Nikiforova,et al.  Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells. , 2000, Science.

[3]  R. Young,et al.  Transcription of eukaryotic protein-coding genes. , 2000, Annual review of genetics.

[4]  H. Kimura,et al.  Specialized transcription factories within mammalian nuclei. , 2000, Critical reviews in eukaryotic gene expression.

[5]  G. Church,et al.  A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression , 2000, Nature Genetics.

[6]  Cameron S. Osborne,et al.  Long-range chromatin regulatory interactions in vivo , 2002, Nature Genetics.

[7]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[8]  Tom Misteli,et al.  Conservation of Relative Chromosome Positioning in Normal and Cancer Cells , 2002, Current Biology.

[9]  R. van Driel,et al.  The eukaryotic genome: a system regulated at different hierarchical levels , 2003, Journal of Cell Science.

[10]  P. Walter,et al.  Gene Recruitment of the Activated INO1 Locus to the Nuclear Membrane , 2004, PLoS biology.

[11]  S. Gasser,et al.  Sir-Mediated Repression Can Occur Independently of Chromosomal and Subnuclear Contexts , 2004, Cell.

[12]  C. Pál,et al.  The evolutionary dynamics of eukaryotic gene order , 2004, Nature Reviews Genetics.

[13]  Antonin Morillon,et al.  Gene loops juxtapose promoters and terminators in yeast , 2004, Nature Genetics.

[14]  P. Jallepalli,et al.  Ufd2, a Novel Autoantigen in Scleroderma, Regulates Sister Chromatid Separation , 2004, Cell cycle.

[15]  S. Teichmann,et al.  Genes Encoding Subunits of Stable Complexes Are Clustered on the Yeast Chromosomes , 2004, Genetics.

[16]  F. Grosveld,et al.  The active spatial organization of the beta-globin locus requires the transcription factor EKLF. , 2004, Genes & development.

[17]  Cameron S. Osborne,et al.  Active genes dynamically colocalize to shared sites of ongoing transcription , 2004, Nature Genetics.

[18]  Pamela A. Silver,et al.  Genome-Wide Localization of the Nuclear Transport Machinery Couples Transcriptional Status and Nuclear Organization , 2004, Cell.

[19]  Tom Misteli,et al.  Tissue-specific spatial organization of genomes , 2004, Genome Biology.

[20]  Thomas Ried,et al.  From Silencing to Gene Expression Real-Time Analysis in Single Cells , 2004, Cell.

[21]  T. Misteli,et al.  Spatial genome organization during T-cell differentiation , 2004, Cytogenetic and Genome Research.

[22]  Tomoharu Kiyuna,et al.  Alteration of chromosome positioning during adipocyte differentiation , 2004, Journal of Cell Science.

[23]  David J. Chen,et al.  Genomic instability in laminopathy-based premature aging , 2005, Nature Medicine.

[24]  Katherine L. Wilson,et al.  The nuclear lamina comes of age , 2005, Nature Reviews Molecular Cell Biology.

[25]  Giorgio Bernardi,et al.  Gene-rich and gene-poor chromosomal regions have different locations in the interphase nuclei of cold-blooded vertebrates , 2006, Chromosoma.

[26]  K. H. Wolfe,et al.  Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. , 2005, Molecular biology and evolution.

[27]  R. Eils,et al.  Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes , 2005, PLoS biology.

[28]  E. Eichler,et al.  Chromosome evolution in eukaryotes: a multi-kingdom perspective. , 2005, Trends in genetics : TIG.

[29]  R. Flavell,et al.  Interchromosomal associations between alternatively expressed loci , 2005, Nature.

[30]  D. Kleinjan,et al.  Long-range control of gene expression: emerging mechanisms and disruption in disease. , 2005, American journal of human genetics.

[31]  M. Groudine,et al.  Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. , 2005, Molecular cell.

[32]  Tom Misteli,et al.  The Cell Nucleus and Aging: Tantalizing Clues and Hopeful Promises , 2005, PLoS biology.

[33]  F. Hediger,et al.  Nuclear pore association confers optimal expression levels for an inducible yeast gene , 2006, Nature.

[34]  M. Fornerod,et al.  Characterization of the Drosophila melanogaster genome at the nuclear lamina , 2006, Nature Genetics.

[35]  Irene K. Moore,et al.  A genomic code for nucleosome positioning , 2006, Nature.

[36]  A. Dean.  On a chromosome far, far away: LCRs and gene expression. , 2006, Trends in genetics : TIG.

[37]  L. Duret,et al.  Evolutionary origin and maintenance of coexpressed gene clusters in mammals. , 2006, Molecular biology and evolution.

[38]  Jean-Christophe Olivo-Marin,et al.  SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope , 2006, Nature.

[39]  I. Sánchez,et al.  Chromosome territory positioning of conserved homologous chromosomes in different primate species , 2006, Chromosoma.

[40]  Malgorzata Schelder,et al.  Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila. , 2006, Molecular cell.

[41]  Bruce D. Smith,et al.  The Molecular Genetics of Crop Domestication , 2006, Cell.

[42]  L. Aravind,et al.  Estimating the Prevalence and Regulatory Potential of the Telomere Looping Effect in Yeast Transcription Regulation , 2006, Cell cycle.

[43]  A. Pombo,et al.  Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations , 2006, PLoS biology.

[44]  S. Liebhaber,et al.  Locus control region transcription plays an active role in long-range gene activation. , 2006, Molecular cell.

[45]  Giacomo Cavalli,et al.  RNAi Components Are Required for Nuclear Clustering of Polycomb Group Response Elements , 2006, Cell.

[46]  Debra T. Burhans,et al.  Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome , 2006, BMC Evolutionary Biology.

[47]  L. Lukens,et al.  Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. , 2006, The Plant journal : for cell and molecular biology.

[48]  Thomas Cremer,et al.  Chromosome territories--a functional nuclear landscape. , 2006, Current opinion in cell biology.

[49]  Richard Axel,et al.  Interchromosomal Interactions and Olfactory Receptor Choice , 2006, Cell.

[50]  Michael Grunstein,et al.  Genome-wide patterns of histone modifications in yeast , 2006, Nature Reviews Molecular Cell Biology.

[51]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[52]  Anne E Carpenter,et al.  Long-Range Directional Movement of an Interphase Chromosome Site , 2006, Current Biology.

[53]  D. Marenduzzo,et al.  Modeling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context. , 2006, Structure.

[54]  Wolfgang Huber,et al.  Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. , 2007, Genomics.

[55]  Yvonne N Fondufe-Mittendorf,et al.  H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State , 2007, PLoS biology.

[56]  A. Arneodo,et al.  Chromosome territories have a highly nonspherical morphology and nonrandom positioning , 2007, Chromosome Research.

[57]  P. Fraser,et al.  Nuclear organization of the genome and the potential for gene regulation , 2007, Nature.

[58]  S. Gasser,et al.  The nuclear envelope and transcriptional control , 2007, Nature Reviews Genetics.

[59]  M. Lipinski,et al.  Chromatin domains and regulation of transcription. , 2007, Journal of molecular biology.

[60]  Tom Misteli,et al.  Cell biology: Chromosome territories , 2007, Nature.

[61]  A. Gregory Matera,et al.  Actin-dependent intranuclear repositioning of an active gene locus in vivo , 2007, The Journal of cell biology.

[62]  S. Otto,et al.  The Evolutionary Consequences of Polyploidy , 2007, Cell.

[63]  F. Grosveld,et al.  Inter-chromosomal gene regulation in the mammalian cell nucleus. , 2007, Current opinion in genetics & development.

[64]  J. Claverie,et al.  Tentative Mapping of Transcription-Induced Interchromosomal Interaction using Chimeric EST and mRNA Data , 2007, PloS one.

[65]  Davide Marenduzzo,et al.  What are the molecular ties that maintain genomic loops? , 2007, Trends in genetics : TIG.

[66]  T. Cremer,et al.  Evolutionarily conserved, cell type and species-specific higher order chromatin arrangements in interphase nuclei of primates , 2007, Chromosoma.

[67]  A. Arneodo,et al.  Chromosome neighborhood composition determines translocation outcomes after exposure to high-dose radiation in primary cells , 2007, Chromosome Research.

[68]  R. Schneider,et al.  Dynamics and interplay of nuclear architecture, genome organization, and gene expression. , 2007, Genes & development.

[69]  Ana Pombo,et al.  Functional organisation of the genome during interphase. , 2007, Current opinion in genetics & development.

[70]  Guillaume J. Filion,et al.  Sensing X Chromosome Pairs Before X Inactivation via a Novel X-Pairing Region of the Xic , 2007, Science.

[71]  K. Sneppen,et al.  Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification , 2007, Cell.

[72]  J. F. Poyatos,et al.  The determinants of gene order conservation in yeasts , 2007, Genome Biology.

[73]  J. McNally,et al.  Organization of chromatin and histone modifications at a transcription site , 2007, The Journal of cell biology.

[74]  T. Cremer,et al.  Biochemistry meets nuclear architecture: multicolor immuno-FISH for co-localization analysis of chromosome segments and differentially expressed gene loci with various histone methylations. , 2007, Advances in enzyme regulation.

[75]  F. Ferrari,et al.  Genomic expression during human myelopoiesis , 2007, BMC Genomics.

[76]  D. Scalzo,et al.  Coordinate Gene Regulation during Hematopoiesis Is Related to Genomic Organization , 2007, PLoS biology.

[77]  Thomas Cremer,et al.  Radial chromatin positioning is shaped by local gene density, not by gene expression , 2007, Chromosoma.

[78]  Cameron S. Osborne,et al.  Myc Dynamically and Preferentially Relocates to a Transcription Factory Occupied by Igh , 2007, PLoS biology.

[79]  Jeannie T. Lee,et al.  Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein , 2007, Nature Genetics.

[80]  A. Pombo.  Advances in imaging the interphase nucleus using thin cryosections , 2007, Histochemistry and Cell Biology.

[81]  T. Misteli.  Beyond the Sequence: Cellular Organization of Genome Function , 2011 .

[82]  Peter J. Lockhart,et al.  Chromatin remodelling is a major source of coexpression of linked genes in yeast , 2007 .

[83]  V. Corces,et al.  The role of insulator elements in large-scale chromatin structure in interphase. , 2007, Seminars in cell & developmental biology.

[84]  D. Geerts,et al.  Domain-wide regulation of gene expression in the human genome. , 2007, Genome research.

[85]  W. D. Laat,et al.  An evaluation of 3C-based methods to capture DNA interactions , 2007, Nature Methods.

[86]  Vinod Subramaniam,et al.  Intracellular manipulation of chromatin using magnetic nanoparticles , 2008, Chromosome Research.

[87]  L. Aravind,et al.  Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal? , 2008, Trends in genetics : TIG.

[88]  E. Stockinger,et al.  A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit , 2008, Science.

[89]  L. Wessels,et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions , 2008, Nature.

[90]  Tiago Branco,et al.  Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH , 2008, Chromosome Research.

[91]  Roger D. Kornberg,et al.  Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription , 2008, Cell.

[92]  Elizabeth Kerr,et al.  Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells , 2008, PLoS genetics.

[93]  Miki Ebisuya,et al.  Ripples from neighbouring transcription , 2008, Nature Cell Biology.

[94]  Peter R. Cook,et al.  Similar active genes cluster in specialized transcription factories , 2008, The Journal of cell biology.

[95]  David L. Spector,et al.  Chromatin Dynamics and Gene Positioning , 2008, Cell.

[96]  D. Thanos,et al.  Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression , 2008, Cell.

[97]  Rutger Hermsen,et al.  Chance and necessity in chromosomal gene distributions. , 2008, Trends in genetics : TIG.

[98]  P. Mieczkowski,et al.  Double-strand breaks associated with repetitive DNA can reshape the genome , 2008, Proceedings of the National Academy of Sciences.

[99]  E. Bertolino,et al.  Transcriptional repression mediated by repositioning of genes to the nuclear lamina , 2008, Nature.

[100]  P. Silver,et al.  Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. , 2008, Genes & development.

[101]  J. Collado-Vides,et al.  Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes , 2008, Proceedings of the National Academy of Sciences.

[102]  Stephan Sauer,et al.  Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms , 2008, Cell.

[103]  T. Mexia,et al.  Author ' s personal copy , 2009 .

[104]  E. Koonin,et al.  Comparative Genomics, Evolution and Origins of the Nuclear Envelope and Nuclear Pore Complex , 2004, Cell cycle.