Genomic Pangea: Coordinate gene regulation and cell-specific chromosomal topologies

Current Opinion in Cell Biology

Volumn 22, Issue 3, 2010, Pages 314-319

  Laster, Kyle ^a   Kosak, Steven T ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DIFFERENTIATION; CELL SPECIFICITY; CHROMOSOMAL LOCALIZATION; CHROMOSOME STRUCTURE; FEEDBACK SYSTEM; GENE CONTROL; GENE EXPRESSION; GENOME ANALYSIS; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; STRUCTURAL GENOMICS; ANIMAL; CHROMOSOME; GENE EXPRESSION REGULATION; GENETICS; GENOME; METABOLISM;

ANIMALS; CHROMOSOMES; GENE EXPRESSION REGULATION; GENOME; HUMANS;

EUKARYOTA;

EID: 77954819009     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ceb.2010.04.009     Document Type: Review

References (35)

1. Kosak S.T., Groudine M. Form follows function: the genomic organization of cellular differentiation. Genes Dev 2004, 18:1371-1384.
2. Cremer T., Kurz A., Zirbel R., Dietzel S., Rinke B., Schrock E., Speicher M.R., Mathieu U., Jauch A., Emmerich P., et al. Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harb Symp Quant Biol 1993, 58:777-792.
3. Mahy N.L., Perry P.E., Gilchrist S., Baldock R.A., Bickmore W.A. Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 2002, 157:579-589.
4. Branco M.R., Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 2006, 4:e138.
5. 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. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 2000, 113(Pt 9):1565-1576.
6. Williams R.R., Broad S., Sheer D., Ragoussis J. Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp Cell Res 2002, 272:163-175.
7. Chambeyron S., Da Silva N.R., Lawson K.A., Bickmore W.A. Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 2005, 132:2215-2223.
8. Ragoczy T., Telling A., Sawado T., Groudine M., Kosak S.T. A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res 2003, 11:513-525.
9. Croft J.A., Bridger J.M., Boyle S., Perry P., Teague P., Bickmore W.A. Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 1999, 145:1119-1131.
10. Bridger J.M., Boyle S., Kill I.R., Bickmore W.A. Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr Biol 2000, 10:149-152.
11. Kosak S.T., Scalzo D., Alworth S.V., Li F., Palmer S., Enver T., Lee J.S., Groudine M. Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol 2007, 5:e309.
12. Gerlich D., Beaudouin J., Kalbfuss B., Daigle N., Eils R., Ellenberg J. Global chromosome positions are transmitted through mitosis in mammalian cells. Cell 2003, 112:751-764.
13. Walter J., Schermelleh L., Cremer M., Tashiro S., Cremer T. Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J Cell Biol 2003, 160:685-697.
14. Thomson I., Gilchrist S., Bickmore W.A., Chubb J.R. The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol 2004, 14:166-172.
15. Simonis M., Klous P., Splinter E., Moshkin Y., Willemsen R., de Wit E., van Steensel B., de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 2006, 38:1348-1354.
16. Zhao Z., Tavoosidana G., Sjolinder M., Gondor A., Mariano P., Wang S., Kanduri C., Lezcano M., Sandhu K.S., Singh U., et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 2006, 38:1341-1347.
17. Guelen L., Pagie L., Brasset E., Meuleman W., Faza M.B., Talhout W., Eussen B.H., de Klein A., Wessels L., de Laat W., et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008, 453:948-951.
18. Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
19. Tanabe H., Kupper K., Ishida T., Neusser M., Mizusawa H. Inter- and intra-specific gene-density-correlated radial chromosome territory arrangements are conserved in Old World monkeys. Cytogenet Genome Res 2005, 108:255-261.
20. Tanabe H., Muller S., Neusser M., von Hase J., Calcagno E., Cremer M., Solovei I., Cremer C., Cremer T. Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci USA 2002, 99:4424-4429.
21. Boyle S., Gilchrist S., Bridger J.M., Mahy N.L., Ellis J.A., Bickmore W.A. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 2001, 10:211-219.
22. Cremer M., von Hase J., Volm T., Brero A., Kreth G., Walter J., Fischer C., Solovei I., Cremer C., Cremer T. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 2001, 9:541-567.
23. Cremer M., Kupper K., Wagler B., Wizelman L., von Hase J., Weiland Y., Kreja L., Diebold J., Speicher M.R., Cremer T. Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol 2003, 162:809-820.
24. Bolzer A., Kreth G., Solovei I., Koehler D., Saracoglu K., Fauth C., Muller S., Eils R., Cremer C., Speicher M.R., et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 2005, 3:e157.
25. Mayer R., Brero A., von Hase J., Schroeder T., Cremer T., Dietzel S. Common themes and cell type specific variations of higher order chromatin arrangements in the mouse. BMC Cell Biol 2005, 6:44.
26. Parada L.A., McQueen P.G., Misteli T. Tissue-specific spatial organization of genomes. Genome Biol 2004, 5:R44.
27. Branco M.R., Branco T., Ramirez F., Pombo A. Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH. Chromosome Res 2008, 16:413-426.
28. Meaburn K.J., Newbold R.F., Bridger J.M. Positioning of human chromosomes in murine cell hybrids according to synteny. Chromosoma 2008, 117:579-591.
29. Sengupta K., Camps J., Mathews P., Barenboim-Stapleton L., Nguyen Q.T., Difilippantonio M.J., Ried T. Position of human chromosomes is conserved in mouse nuclei indicating a species-independent mechanism for maintaining genome organization. Chromosoma 2008, 117:499-509.
30. Rajapakse I., Perlman M.D., Scalzo D., Kooperberg C., Groudine M., Kosak S.T. The emergence of lineage-specific chromosomal topologies from coordinate gene regulation. Proc Natl Acad Sci USA 2009, 106:6679-6684.
31. Bártová E., Krejcí J., Harnicarová A., Kozubek S. Differentiation of human embryonic stem cells induces condensation of chromosome territories and formation of heterochromatin protein 1 foci. Differentiation 2008, 76:24-32.
32. Gaspar-Maia A., Alajem A., Polesso F., Sridharan R. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 2009, 460:863-868.
33. Taimen P., Pfleghaar K., Shimi T., Möller D. A progeria mutation reveals functions for lamin A in nuclear assembly, architecture, and chromosome organization. Proc Natl Acad Sci USA 2009, 106:20788-20793.
34. Meaburn K.J., Misteli T. Locus-specific and activity-independent gene repositioning during early tumorigenesis. J Cell Biol 2008, 180:39-50.
35. Marella N.V., Bhattacharya S., et al. Cell type specific chromosome territory organization in the interphase nucleus of normal and cancer cells. J Cell Physiol 2009, 221(1):130-138.