Chromosome territories – a functional nuclear landscape

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

Cremer, T., & Cremer, C. (2001) · Nature Reviews Genetics · doi:10.1038/35066075 · Cited by 2,328

The diverse functions of histone lysine methylation

Martin, C., & Zhang, Y. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1761 · Cited by 2,057

DNA methylation and gene silencing in cancer

Baylin, S. B. (2005) · Nature Clinical Practice Oncology · doi:10.1038/ncponc0354 · Cited by 1,154

Nuclear structure in cancer cells

Zink, D., Fischer, A. H., & Nickerson, J. A. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1430 · Cited by 1,068

Active genes dynamically colocalize to shared sites of ongoing transcription

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A Morphological Distinction between Neurones of the Male and Female, and the Behaviour of the Nucleolar Satellite during Accelerated Nucleoprotein Synthesis

BARR, M. L., & BERTRAM, E. G. (1949) · Nature · doi:10.1038/163676a0 · Cited by 1,030

Differences in the Localization and Morphology of Chromosomes in the Human Nucleus

Croft, J. A., Bridger, J. M., Boyle, S., Perry, P., Teague, P., & Bickmore, W. A. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.145.6.1119 · Cited by 933

Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes

Bolzer, A., Kreth, G., Solovei, I., Koehler, D., Saracoglu, K., Fauth, C., Müller, S., Eils, R., Cremer, C., Speicher, M. R., et al. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030157 · Cited by 837

The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains

Caron, H., Schaik, B. V., Mee, M. V. D., Baas, F., Riggins, G., Sluis, P. V., Hermus, M.-C., Asperen, R. V., Boon, K., Voûte, P. A., et al. (2001) · Science · doi:10.1126/science.1056794 · Cited by 731

Interchromosomal associations between alternatively expressed loci

Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R., & Flavell, R. A. (2005) · Nature · doi:10.1038/nature03574 · Cited by 730

The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells

Boyle, S. (2001) · Human Molecular Genetics · doi:10.1093/hmg/10.3.211 · Cited by 691

DNA methylation and histone modifications: teaming up to silence genes

Fuks, F. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.08.002 · Cited by 644

Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription

Chambeyron, S., & Bickmore, W. A. (2004) · Genes & Development · doi:10.1101/gad.292104 · Cited by 623

Chromatin Architecture of the Human Genome

Gilbert, N., Boyle, S., Fiegler, H., Woodfine, K., Carter, N. P., & Bickmore, W. A. (2004) · Cell · doi:10.1016/j.cell.2004.08.011 · Cited by 501

Role of Chromosome Territories in the Functional Compartmentalization of the Cell Nucleus

Cremer, T., Kurz, A., Zirbel, R., Dietzel, S., Rinke, B., Schrock, E., Speicher, M. R., Mathieu, U., Jauch, A., Emmerich, P., et al. (1993) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1993.058.01.085 · Cited by 488

Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei

Volpi, E. V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J., Beck, S., Campbell, R. D., Goldsworthy, M., Powis, S. H., Ragoussis, J., et al. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.9.1565 · Cited by 441

Spatial proximity of translocation-prone gene loci in human lymphomas

Roix, J. J., McQueen, P. G., Munson, P. J., Parada, L. A., & Misteli, T. (2003) · Nature Genetics · doi:10.1038/ng1177 · Cited by 414

Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates

Tanabe, H., Müller, S., Neusser, M., von Hase, J., Calcagno, E., Cremer, M., Solovei, I., Cremer, C., & Cremer, T. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.072618599 · Cited by 399

Transient Homologous Chromosome Pairing Marks the Onset of X Inactivation

Xu, N., Tsai, C.-L., & Lee, J. T. (2006) · Science · doi:10.1126/science.1122984 · Cited by 380

Architecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage

Kettenberger, H., Armache, K.-J., & Cramer, P. (2003) · Cell · doi:10.1016/s0092-8674(03)00598-1 · Cited by 355

The Dynamics of Chromosome Organization and Gene Regulation

Spector, D. L. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161724 · Cited by 341

Visualization of G1 chromosomes: a folded, twisted, supercoiled chromonema model of interphase chromatid structure.

Belmont, A. S., & Bruce, K. (1994) · The Journal of cell biology · doi:10.1083/jcb.127.2.287 · Cited by 340

Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages

Walter, J., Schermelleh, L., Cremer, M., Tashiro, S., & Cremer, T. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200211103 · Cited by 322

Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation

Bacher, C. P., Guggiari, M., Brors, B., Augui, S., Clerc, P., Avner, P., Eils, R., & Heard, E. (2006) · Nature Cell Biology · doi:10.1038/ncb1365 · Cited by 321

A random-walk/giant-loop model for interphase chromosomes.

Sachs, R. K., van den Engh, G., Trask, B., Yokota, H., & Hearst, J. E. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.7.2710 · Cited by 301

Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH

Mahy, N. L., Perry, P. E., & Bickmore, W. A. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200207115 · Cited by 293

Form follows function: the genomic organization of cellular differentiation

Kosak, S. T., & Groudine, M. (2004) · Genes & Development · doi:10.1101/gad.1209304 · Cited by 293

Chromosome Territories, Interchromatin Domain Compartment, and Nuclear Matrix: An Integrated View of the Functional Nuclear Architecture

Cremer, T., Kreth, G., Koester, H., Fink, R. H. A., Heintzmann, R., Cremer, M., Solovei, I., Zink, D., & Cremer, C. (2000) · Critical Reviews™ in Eukaryotic Gene Expression · doi:10.1615/critreveukargeneexpr.v10.i2.60 · Cited by 285

Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

Yokota, H., van den Engh, G., Hearst, J. E., Sachs, R. K., & Trask, B. J. (1995) · The Journal of cell biology · doi:10.1083/jcb.130.6.1239 · Cited by 285

ASSEMBLY OF VARIANT HISTONES INTO CHROMATIN

Henikoff, S., & Ahmad, K. (2005) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.21.012704.133518 · Cited by 278

Inheritance of gene density–related higher order chromatin arrangements in normal and tumor cell nuclei

Cremer, M., Küpper, K., Wagler, B., Wizelman, L., Hase, J. V., Weiland, Y., Kreja, L., Diebold, J., Speicher, M. R., & Cremer, T. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200304096 · Cited by 261

Ultrastructural Analysis of Transcription and Splicing in the Cell Nucleus after Bromo-UTP Microinjection

Cmarko, D., Verschure, P. J., Martin, T. E., Dahmus, M. E., Krause, S., Fu, X.-D., van Driel, R., & Fakan, S. (1999) · Molecular Biology of the Cell · doi:10.1091/mbc.10.1.211 · Cited by 252

Spatial Relationship between Transcription Sites and Chromosome Territories

Verschure, P. J., van der Kraan, I., Manders, E. M. M., & van Driel, R. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.147.1.13 · Cited by 250

Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries

Zirbel, R. M., Mathieu, U. R., Kurz, A., Cremer, T., & Lichter, P. (1993) · Chromosome Research · doi:10.1007/bf00710032 · Cited by 240

Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

Mayer, R., Brero, A., von Hase, J., Schroeder, T., Cremer, T., & Dietzel, S. (2005) · BMC Cell Biology · doi:10.1186/1471-2121-6-44 · Cited by 233

Localisation of rapidly and slowly labelled nuclear RNA as visualized by high resolution autoradiography

Fakan, S., & Bernhard, W. (1971) · Experimental Cell Research · doi:10.1016/0014-4827(71)90628-8 · Cited by 232

Spatial organization of active and inactive genes and noncoding DNA within chromosome territories

Mahy, N. L., Perry, P. E., Gilchrist, S., Baldock, R. A., & Bickmore, W. A. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200111071 · Cited by 225

Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure.

Eils, R., Dietzel, S., Bertin, E., Schröck, E., Speicher, M. R., Ried, T., Robert‐Nicoud, M., Cremer, C. G., & Cremer, T. J. (1996) · The Journal of Cell Biology · doi:10.1083/jcb.135.6.1427 · Cited by 221

The Dynamics of Chromatin Remodeling at Promoters

Mellor, J. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.06.023 · Cited by 219

Subchromosomal Positioning of the Epidermal Differentiation Complex (EDC) in Keratinocyte and Lymphoblast Interphase Nuclei

Williams, R. R. E., Broad, S., Sheer, D., & Ragoussis, J. (2002) · Experimental Cell Research · doi:10.1006/excr.2001.5400 · Cited by 209

Compartmentalization of Interphase Chromosomes Observed in Simulation and Experiment

Münkel, C., Eils, R., Dietzel, S., Zink, D., Mehring, C., Wedemann, G., Cremer, T., & Langowski, J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2361 · Cited by 204

Nuclear re-organisation of the Hoxb complex during mouse embryonic development

Chambeyron, S., Da Silva, N. R., Lawson, K. A., & Bickmore, W. A. (2005) · Development · doi:10.1242/dev.01813 · Cited by 201

Die Blastomerenkerne von Ascaris Megalocephala und die Theorie der Chromosomenindividualität

Boveri, T. (1909) · W. Engelmann eBooks · Cited by 188

The genome and the nucleus: a marriage made by evolution: Genome organisation and nuclear architecture

Foster, H. A., & Bridger, J. M. (2005) · Chromosoma · doi:10.1007/s00412-005-0016-6 · Cited by 181

Spatial Positioning

Misteli, T. (2004) · Cell · doi:10.1016/j.cell.2004.09.035 · Cited by 169

A role for macromolecular crowding effects in the assembly and function of compartments in the nucleus

Hancock, R. (2004) · Journal of Structural Biology · doi:10.1016/j.jsb.2003.12.008 · Cited by 169

Epigenetic aspects of differentiation

Arney, K. L., & Fisher, A. G. (2004) · Journal of Cell Science · doi:10.1242/jcs.01390 · Cited by 165

Higher order chromatin architecture in the cell nucleus: on the way from structure to function

Cremer, T., Küpper, K., Dietzel, S., & Fakan, S. (2004) · Biology of the Cell · doi:10.1016/j.biolcel.2004.07.002 · Cited by 159

The nuclear matrix revealed by eluting chromatin from a cross-linked nucleus

Nickerson, J. A., Krockmalnic, G., Wan, K. M., & Penman, S. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4446 · Cited by 158

Chromatin Organization in the Mammalian Nucleus

Gilbert, N., Gilchrist, S., & Bickmore, W. A. (2004) · International review of cytology · doi:10.1016/s0074-7696(04)42007-5 · Cited by 156

Considering Nuclear Compartmentalization in the Light of Nuclear Dynamics

Chubb, J. R., & Bickmore, W. A. (2003) · Cell · doi:10.1016/s0092-8674(03)00078-3 · Cited by 136

Gene Order and Dynamic Domains

Kosak, S. T., & Groudine, M. T. (2004) · Science · doi:10.1126/science.1103864 · Cited by 134

Alteration of chromosome positioning during adipocyte differentiation

Kuroda, M., Tanabe, H., Yoshida, K., Oikawa, K., Saito, A., Kiyuna, T., Mizusawa, H., & Mukai, K. (2004) · Journal of Cell Science · doi:10.1242/jcs.01508 · Cited by 115

Radial Arrangement of Chromosome Territories in Human Cell Nuclei: A Computer Model Approach Based on Gene Density Indicates a Probabilistic Global Positioning Code

Kreth, G., Schwarz‐Finsterle, J., Hase, J. V., Cremer, M., & Cremer, C. G. (2004) · Biophysical Journal · doi:10.1016/s0006-3495(04)74333-7 · Cited by 115

Spatial genome organization

Parada, L. A. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.03.013 · Cited by 89

Topology of genes and nontranscribed sequences in human interphase nuclei

Scheuermann, M. O., Tajbakhsh, J., Kurz, A., Saracoglu, K., Eils, R., & Lichter, P. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.08.031 · Cited by 86

Silence of the genes — mechanisms of long-term repression

Lande‐Diner, L., & Cedar, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1639 · Cited by 82

The temporal program of DNA replication: new insights into old questions

Zink, D. (2006) · Chromosoma · doi:10.1007/s00412-006-0062-8 · Cited by 73

The functional architecture of the nucleus as analysed by ultrastructural cytochemistry

Fakan, S. (2004) · Histochemistry and Cell Biology · doi:10.1007/s00418-004-0681-1 · Cited by 71

MISE EN EVIDENCE DE L'ADN ET DES POLYSACCHARIDES A L'AIDE D'UN NOUVEAU REACTIF "DE TYPE SCHIFF"

Cogliati, R., & Gauthier, A. (1973) · Cited by 70

Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments

Görisch, S. M., Lichter, P., & Rippe, K. (2005) · Histochemistry and Cell Biology · doi:10.1007/s00418-005-0752-y · Cited by 67

Ultrastructural cytochemical analyses of nuclear functional architecture.

Fakan, S. (2004) · PubMed · doi:10.4081/854 · Cited by 66

The architecture of chicken chromosome territories changes during differentiation

Stadler, S. C., Schnapp, V., Mayer, R., Stein, S., Cremer, C. G., Bonifer, C., Cremer, T. J., & Dietzel, S. (2004) · BMC Cell Biology · doi:10.1186/1471-2121-5-44 · Cited by 66

Local gene density predicts the spatial position of genetic loci in the interphase nucleus

Murmann, A. E., Gao, J., Encinosa, M., Gautier, M., Peter, M. E., Eils, R., Lichter, P., & Rowley, J. D. (2005) · Experimental Cell Research · doi:10.1016/j.yexcr.2005.07.020 · Cited by 66

Nuclear architecture and genome functioning in plants and animals: what can we learn from both?

VANDRIEL, R., & Fransz, P. F. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.03.009 · Cited by 53

The 3D structure of human chromosomes in cell nuclei

Lukášová, E., Kozubek, S., Kozubek, M., Falk, M., & Amrichová, J. (2002) · Chromosome Research · doi:10.1023/a:1020958517788 · Cited by 51

Inter- and intra-specific gene-density-correlated radial chromosome territory arrangements are conserved in Old World monkeys

Tanabe, H., Küpper, K., Ishida, T., Neusser, M., & Mizusawa, H. (2004) · Cytogenetic and Genome Research · doi:10.1159/000080824 · Cited by 50

Cell-by-Cell Dissection of Gene Expression and Chromosomal Interactions Reveals Consequences of Nuclear Reorganization

Harmon, B., & Sedat, J. W. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030067 · Cited by 50

The spatial organization of the genome in mammalian cells

Pederson, T. (2004) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2004.02.008 · Cited by 45

To the 30-nm chromatin fiber and beyond

Adkins, N. L., Watts, M., & Georgel, P. T. (2003) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/j.bbaexp.2003.09.013 · Cited by 39

Comparative analysis of the functional genome architecture of animal andplant cell nuclei

Mayr, C., Jasencakova, Z., Meister, A., Schubert, I. A., & Zink, D. (2003) · Chromosome Research · doi:10.1023/a:1024978711705 · Cited by 36

DNA replication and nuclear architecture

Jaunin, F., & Fakan, S. (2002) · Journal of Cellular Biochemistry · doi:10.1002/jcb.10115 · Cited by 35

Avian genomes: different karyotypes but a similar distribution of the GC-richest chromosome regions at interphase

Federico, C., Cantarella, C. D., Scavo, C., Saccone, S., Bed’Hom, B., & Bernardi, G. (2005) · Chromosome Research · doi:10.1007/s10577-005-1012-7 · Cited by 27

Chromatin Remodeling Factors and DNA Replication

Varga‐Weisz, P. (2005) · Springer eBooks · doi:10.1007/3-540-27310-7_1 · Cited by 23

The epigenome as a molecular marker and target

Gius, D. R., Bradbury, C. M., Sun, L., Awwad, R. T., Huang, L., Smart, D. D., Bisht, K. S., Ho, A. S., & Nguyen, P. (2005) · Cancer · doi:10.1002/cncr.21395 · Cited by 23

Close encounters between active genes in the nucleus.

Chuang, C.-H., & Belmont, A. S. (2005) · Genome biology · doi:10.1186/gb-2005-6-11-237 · Cited by 21

The impact of translocations and gene fusions on cancer causation

Mitelman, F., Johansson, B., & Mertens, F. (2007) · Nature Reviews Cancer · doi:10.1038/nrc2091 · Cited by 1,400

Regulation of DNA double-strand break repair pathway choice

Shrivastav, M., De Haro, L. P., & Nickoloff, J. A. (2008) · Cell Research · doi:10.1038/cr.2007.111 · Cited by 1,329

The selection and function of cell type-specific enhancers

Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010

Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin

Dechat, T., Pfleghaar, K., Sengupta, K., Shimi, T., Shumaker, D. K., Solimando, L., & Goldman, R. D. (2008) · Genes & Development · doi:10.1101/gad.1652708 · Cited by 940

Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions

Lanctôt, C., Cheutin, T., Cremer, M., Cavalli, G., & Cremer, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2041 · Cited by 781