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Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes
Open accessAbstract
Studies of higher-order chromatin arrangements are an essential part of ongoing attempts to explore changes in epigenome structure and their functional implications during development and cell differentiation. However, the extent and cell-type-specificity of three-dimensional (3D) chromosome arrangements has remained controversial. In order to overcome technical limitations of previous studies, we have developed tools that allow the quantitative 3D positional mapping of all chromosomes simultaneously. We present unequivocal evidence for a probabilistic 3D order of prometaphase chromosomes, as well as of chromosome territories (CTs) in nuclei of quiescent (G0) and cycling (early S-phase) human diploid fibroblasts (46, XY). Radial distance measurements showed a probabilistic, highly nonrandom correlation with chromosome size: small chromosomes-independently of their gene density-were distributed significantly closer to the center of the nucleus or prometaphase rosette, while large chromosomes were located closer to the nuclear or rosette rim. This arrangement was independently confirmed in both human fibroblast and amniotic fluid cell nuclei. Notably, these cell types exhibit flat-ellipsoidal cell nuclei, in contrast to the spherical nuclei of lymphocytes and several other human cell types, for which we and others previously demonstrated gene-density-correlated radial 3D CT arrangements. Modeling of 3D CT arrangements suggests that cell-type-specific differences in radial CT arrangements are not solely due to geometrical constraints that result from nuclear shape differences. We also found gene-density-correlated arrangements of higher-order chromatin shared by all human cell types studied so far. Chromatin domains, which are gene-poor, form a layer beneath the nuclear envelope, while gene-dense chromatin is enriched in the nuclear interior. We discuss the possible functional implications of this finding.
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Cites
Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications
Freshney, R. I. (2010) · Wiley eBooks · doi:10.1002/9780470649367 · Cited by 3,870
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
Self-citationGoldman, R. D., Shumaker, D. K., Erdos, M. R., Eriksson, M., Goldman, A. E., Gordon, L. B., Gruenbaum, Y., Khuon, S., Mendez, M., Varga, R., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402943101 · Cited by 1,103
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
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
Parameters of the human genome.
Morton, N. E. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.17.7474 · Cited by 516
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
Self-citationO'Keefe, R. T., Henderson, S. C., & Spector, D. L. (1992) · The Journal of cell biology · doi:10.1083/jcb.116.5.1095 · Cited by 482
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
Self-citationNon-random radial higher-order chromatin arrangements in nuclei of diploid human cells
Cremer, M., von Hase, J., Volm, T., Brero, A., Kreth, G., Walter, J., Fischer, C., Solovei, I., Cremer, C., & Cremer, T. (2001) · Chromosome Research · doi:10.1023/a:1012495201697 · Cited by 393
Self-citationTissue-specific spatial organization of genomes
Parada, L. A., McQueen, P. G., & Misteli, T. (2004) · Genome Biology · doi:10.1186/gb-2004-5-7-r44 · Cited by 377
Integration of cytogenetic landmarks into the draft sequence of the human genome
BAC Resource Consortium, T., Cheung, V. G., Nowak, N., Jang, W., Kirsch, I. R., Zhao, S., Chen, X.-N., Furey, T. S., Kim, U.-J., Kuo, W.-L., et al. (2001) · Nature · doi:10.1038/35057192 · Cited by 316
Chromosome positioning in the interphase nucleus
Parada, L. A., & Misteli, T. (2002) · Trends in Cell Biology · doi:10.1016/s0962-8924(02)02351-6 · Cited by 312
Nuclear Organization of Mammalian Genomes
Sadoni, N., Langer, S., Fauth, C., Bernardi, G., Cremer, T., Turner, B. M., & Zink, D. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.146.6.1211 · Cited by 303
Self-citationForm follows function: the genomic organization of cellular differentiation
Kosak, S. T., & Groudine, M. (2004) · Genes & Development · doi:10.1101/gad.1209304 · Cited by 293
Global Chromosome Positions Are Transmitted through Mitosis in Mammalian Cells
Gerlich, D., Beaudouin, J., Kalbfuss, B., Daigle, N., Eils, R., & Ellenberg, J. (2003) · Cell · doi:10.1016/s0092-8674(03)00189-2 · Cited by 290
Self-citationCremer, 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
Self-citationRe-modelling of nuclear architecture in quiescent and senescent human fibroblasts
Bridger, J. M., Boyle, S., Kill, I. R., & Bickmore, W. A. (2000) · Current Biology · doi:10.1016/s0960-9822(00)00312-2 · Cited by 274
Solovei, I., Cavallo, A., Schermelleh, L., Jaunin, F., Scasselati, C., Cmarko, D., Cremer, C., Fakan, S., & Cremer, T. (2002) · Experimental Cell Research · doi:10.1006/excr.2002.5513 · Cited by 268
Self-citationCremer, 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
Self-citationSize-Dependent Positioning of Human Chromosomes in Interphase Nuclei
Sun, H. B., Shen, J., & Yokota, H. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76282-5 · Cited by 234
Raharjo, W. H., Enarson, P., Sullivan, T., Stewart, C. L., & Burke, B. (2001) · Journal of Cell Science · doi:10.1242/jcs.114.24.4447 · Cited by 230
Arrangements of macro- and microchromosomes in chicken cells
Habermann, F. A., Cremer, M., Walter, J., Kreth, G., von Hase, J., Bauer, K., Wienberg, J., Cremer, C., Cremer, T., & Solovei, I. (2001) · Chromosome Research · doi:10.1023/a:1012447318535 · Cited by 212
Self-citationCompartmentalization 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
Self-citationWeierich, C., Brero, A., Stein, S., von Hase, J., Cremer, C., Cremer, T., & Solovei, I. (2003) · Chromosome Research · doi:10.1023/a:1025016828544 · Cited by 189
Self-citationThe eukaryotic genome: a system regulated at different hierarchical levels
van Driel, R., Fransz, P. F., & Verschure, P. J. (2003) · Journal of Cell Science · doi:10.1242/jcs.00779 · Cited by 179
Precise Spatial Positioning of Chromosomes During Prometaphase: Evidence for Chromosomal Order
Nagele, R., Freeman, T., McMorrow, L., & Lee, H.-Y. (1995) · Science · doi:10.1126/science.270.5243.1831 · Cited by 166
Tanabe, H., Habermann, F. A., Solovei, I., Cremer, M., & Cremer, T. (2002) · Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis · doi:10.1016/s0027-5107(02)00077-5 · Cited by 164
Self-citationHigher 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
Self-citationHarnden, D. G., & Klinger, H. P. (1985) · Medical Entomology and Zoology · Cited by 136
Eils, R., Uhrig, S., Saracoglu, K., Sätzler, K., Bolzer, A., Petersen, I., Chassery, J., Ganser, M. H., & Speicher, M. R. (1998) · Cytogenetic and Genome Research · doi:10.1159/000015092 · Cited by 123
Self-citationKreth, 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
Self-citationChromosomes exhibit preferential positioning in nuclei of quiescent human cells
Nagele, R. G., Freeman, T. A., McMorrow, L. E., Thomson, Z., Kitson-Wind, K., & Lee, H. (1999) · Journal of Cell Science · doi:10.1242/jcs.112.4.525 · Cited by 102
Radiation‐induced chromosome aberrations: Insights gained from biophysical modeling
Hlatky, L., Sachs, R. K., Vázquez, M., & Cornforth, M. N. (2002) · BioEssays · doi:10.1002/bies.10126 · Cited by 98
Müller, S., & Wienberg, J. (2001) · Human Genetics · doi:10.1007/s004390100535 · Cited by 96
Self-citationChromosomes are predominantly located randomly with respect to each other in interphase human cells
Cornforth, M. N., Greulich‐Bode, K. M., Loucas, B. D., Arsuaga, J., Vázquez, M., Sachs, R. K., Brückner, M., Molls, M., Hahnfeldt, P., Hlatky, L., et al. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200206009 · Cited by 95
The compositional evolution of vertebrate genomes
Bernardi, G. (2000) · Gene · doi:10.1016/s0378-1119(00)00441-8 · Cited by 90
Parada, L. A. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.03.013 · Cited by 89
FISH on three-dimensionally preserved nuclei
Solovei, I. V., Walter, J., Cremer, M., Habermann, F. A., Schermelleh, L., & Cremer, T. J. (2002) · doi:10.1093/oso/9780199638833.003.0007 · Cited by 70
Self-citationAn uncertainty principle in chromosome positioning
Parada, L. A., Roix, J. J., & Misteli, T. (2003) · Trends in Cell Biology · doi:10.1016/s0962-8924(03)00149-1 · Cited by 70
Towards unlimited colors for fluorescence in-situ hybridization (FISH)
Müller, S., Neusser, M., & Wienberg, J. (2002) · Chromosome Research · doi:10.1023/a:1015296122470 · Cited by 61
Self-citationBuffering: a Possible Passive-homeostasis Role for Redundant DNA
Vinogradov, A. E. (1998) · Journal of Theoretical Biology · doi:10.1006/jtbi.1997.0629 · Cited by 49
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
Chromosome spatial order in human cells: evidence for early origin and faithful propagation
Nagele, R. G., Freeman, T. A., Fazekas, J., Lee, K.-M., Thomson, Z., & Lee, H.-Y. (1998) · Chromosoma · doi:10.1007/s004120050315 · Cited by 45
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
Position of chromosomes in the human interphase nucleus
Hager, H. D., Schroeder-Kurth, T. M., & Vogel, F. (1982) · Human Genetics · doi:10.1007/bf00276599 · Cited by 31
Koss, L. G. (1998) · Cytogenetic and Genome Research · doi:10.1159/000015109 · Cited by 21
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Harnessing nanotopography and integrin–matrix interactions to influence stem cell fate
Dalby, M. J., Gadegaard, N., & Oreffo, R. O. C. (2014) · Nature Materials · doi:10.1038/nmat3980 · Cited by 1,082
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
Self-citationNuclear organization of the genome and the potential for gene regulation
Fraser, P., & Bickmore, W. (2007) · Nature · doi:10.1038/nature05916 · Cited by 734
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B., & Zhuang, X. (2020) · Cell · doi:10.1016/j.cell.2020.07.032 · Cited by 562
Regulation of genome organization and gene expression by nuclear mechanotransduction
Uhler, C., & Shivashankar, G. V. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.101 · Cited by 445
Metadata
- Authors
- Bolzer, A., Kreth, G., Solovei, I., Koehler, D., Saracoglu, K., Fauth, C., Müller, S., Eils, R., Cremer, C., Speicher, M. R., & Cremer, T.
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2005-04-26
- Volume
- 3
- Issue
- 5
- Pages
- e157
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2092499706
- Cited by
- 837
- References
- 48
- FWCI
- 14.98
- Type
- journal article
- Language
- en
- Open access
- gold
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