Nuclear genome organization: common themes and individual patterns

Current Opinion in Genetics and Development

Volumn 19, Issue 2, 2009, Pages 166-171

  Fedorova, Elena ^a,b   Zink, Daniele ^c  

^a PAVLOV INSTITUTE OF PHYSIOLOGY   (Russian Federation)

^b INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^c INSTITUTE OF BIOENGINEERING AND NANOTECHNOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME STRUCTURE; DNA SEQUENCE; GENE ACTIVITY; GENE CONTROL; GENE LOCATION; GENE LOCUS; GENE SILENCING; GENOME ANALYSIS; HUMAN; NONHUMAN; NUCLEAR LAMINA; NUCLEAR PORE; PRIORITY JOURNAL; REVIEW;

ANIMALS; CELL NUCLEUS; CHROMOSOME POSITIONING; GENE EXPRESSION REGULATION; GENOME; HUMANS; MODELS, BIOLOGICAL; NUCLEAR ENVELOPE; NUCLEAR PROTEINS; PROTEIN BINDING;

EID: 65449128866     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2009.02.003     Document Type: Review

References (48)

1. Chakalova L., Debrand E., Mitchell J.A., Osborne C.S., and Fraser P. Replication and transcription: shaping the landscape of the genome. Nat Rev Genet 6 (2005) 669-677
2. Janga S.C., Collado-Vides J., and Babu M.M. Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes. Proc Natl Acad Sci U S A 105 (2008) 15761-15766
3. Sproul D., Gilbert N., and Bickmore W.A. The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet 6 (2005) 775-781
4. de Wit E., Braunschweig U., Greil F., Bussemaker H.J., and van Steensel B. Global chromatin domain organization of the Drosophila genome. PLoS Genet 4 (2008) e1000045
5. Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., Wei G., Chepelev I., and Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837
6. Jeppesen P., and Turner B.M. The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74 (1993) 281-289
7. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
8. Smith Z.E., and Higgs D.R. The pattern of replication at a human telomeric region (16p13.3): its relationship to chromosome structure and gene expression. Hum Mol Genet 8 (1999) 1373-1386
9. Vyas P., Vickers M.A., Simmons D.L., Ayyub H., Craddock C.F., and Higgs D.R. Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. Cell 69 (1992) 781-793
10. Azuara V., Perry P., Sauer S., Spivakov M., Jorgensen H.F., John R.M., Gouti M., Casanova M., Warnes G., Merkenschlager M., et al. Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8 (2006) 532-538. This study demonstrates that the pluripotency of ES cells is associated with a specific epigenetic profile where lineage-specific genes display H3K27 trimethylation in combination with histone marks typically associated with active chromatin.
11. Giadrossi S., Dvorkina M., and Fisher A.G. Chromatin organization and differentiation in embryonic stem cell models. Curr Opin Genet Dev 17 (2007) 132-138
12. Hiratani I., Ryba T., Itoh M., Yokochi T., Schwaiger M., Chang C.W., Lyou Y., Townes T.M., Schubeler D., and Gilbert D.M. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6 (2008) e245. This is a detailed analysis of replication domains in murine iPS and ES cells and in neural precursor cells derived from ES cells. The results show that replication domains consolidate during differentiation.
13. Fedorova E., and Zink D. Nuclear architecture and gene regulation. Biochim Biophys Acta 1783 (2008) 2174-2184
14. Pickersgill H., Kalverda B., de Wit E., Talhout W., Fornerod M., and van Steensel B. Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38 (2006) 1005-1014
15. 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 453 (2008) 948-951. This study provides a genome-wide analysis of lamina interactions in human cells. The results show that large chromosomal domains with sharp boundaries interact with the lamina. These domains provide a highly repressive chromatin environment.
16. Takizawa T., Gudla P.R., Guo L., Lockett S., and Misteli T. Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. Genes Dev 22 (2008) 489-498
17. Finlan L.E., Sproul D., Thomson I., Boyle S., Kerr E., Perry P., Ylstra B., Chubb J.R., and Bickmore W.A. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4 (2008) e1000039. This report is one of the three recent studies analyzing the effects of gene tethering to the periphery of mammalian nuclei.
18. Kumaran R.I., and Spector D.L. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol 180 (2008) 51-65. This report is one of the three recent studies analyzing the effects of gene tethering to the periphery of mammalian nuclei.
19. Reddy K.L., Zullo J.M., Bertolino E., and Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452 (2008) 243-247. This report is one of the three recent studies analyzing the effects of gene tethering to the periphery of mammalian nuclei.
20. Sadoni N., Targosz B.S., Englmann A., Fesser S., Koch J., Schindelhauer D., and Zink D. Transcription-dependent spatial arrangements of CFTR and conserved adjacent loci are not conserved in human and murine nuclei. Chromosoma 117 (2008) 381-397
21. Yasuhara J.C., and Wakimoto B.T. Oxymoron no more: the expanding world of heterochromatic genes. Trends Genet 22 (2006) 330-338
22. Zink D. The temporal program of DNA replication: new insights into old questions. Chromosoma 115 (2006) 273-287
23. Mekhail K., Seebacher J., Gygi S.P., and Moazed D. Role for perinuclear chromosome tethering in maintenance of genome stability. Nature 456 (2008) 667-670
24. Akhtar A., and Gasser S.M. The nuclear envelope and transcriptional control. Nat Rev Genet 8 (2007) 507-517
25. Kurshakova M.M., Krasnov A.N., Kopytova D.V., Shidlovskii Y.V., Nikolenko J.V., Nabirochkina E.N., Spehner D., Schultz P., Tora L., and Georgieva S.G. SAGA and a novel Drosophila export complex anchor efficient transcription and mRNA export to NPC. EMBO J 26 (2007) 4956-4965
26. Casolari J.M., Brown C.R., Komili S., West J., Hieronymus H., and Silver P.A. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117 (2004) 427-439
27. Brown C.R., Kennedy C.J., Delmar V.A., Forbes D.J., and Silver P.A. Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. Genes Dev 22 (2008) 627-639. This is the first chromosome-wide analysis of nuclear pore interactions in mammalian cells. It is demonstrated that nuclear pore interactions are highly dynamic and depend on histone acetylation patterns.
28. Zink D., Amaral M.D., Englmann A., Lang S., Clarke L.A., Rudolph C., Alt F., Luther K., Braz C., Sadoni N., et al. Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166 (2004) 815-825
29. Dekker J., Rippe K., Dekker M., and Kleckner N. Capturing chromosome conformation. Science 295 (2002) 1306-1311
30. Dostie J., and Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2 (2007) 988-1002
31. Dostie J., Richmond T.A., Arnaout R.A., Selzer R.R., Lee W.L., Honan T.A., Rubio E.D., Krumm A., Lamb J., Nusbaum C., et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16 (2006) 1299-1309
32. Simonis M., Klous P., Splinter E., Moshkin Y., Willemsen R., de Wit E., van Steensel B., and de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38 (2006) 1348-1354
33. 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 38 (2006) 1341-1347
34. Apostolou E., and Thanos D. Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell 134 (2008) 85-96
35. Tiwari V.K., Cope L., McGarvey K.M., Ohm J.E., and Baylin S.B. A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res 18 (2008) 1171-1179
36. Fraser P., and Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature 447 (2007) 413-417
37. Branco M.R., and Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 4 (2006) e138
38. Kosak S.T., Scalzo D., Alworth S.V., Li F., Palmer S., Enver T., Lee J.S., and Groudine M. Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol 5 (2007) e309
39. Parada L., and Misteli T. Chromosome positioning in the interphase nucleus. Trends Cell Biol 12 (2002) 425-432
40. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods 3 (2006) 17-21
41. de Laat W. Long-range DNA contacts: romance in the nucleus?. Curr Opin Cell Biol 19 (2007) 317-320
42. Brown J.M., Green J., das Neves R.P., Wallace H.A., Smith A.J., Hughes J., Gray N., Taylor S., Wood W.G., Higgs D.R., et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 182 (2008) 1083-1097. Detailed and careful analysis of the spatial organization of human globin loci and the dependence of their organization on transcriptional activity and the chromosomal environment. The results provide evidence that the frequent spatial proximity of globin loci in cells where these are transcriptionally active is due to their association with splicing speckles but does not reflect functional interactions between these loci or sharing of a common transcription factory.
43. Brown J.M., Leach J., Reittie J.E., Atzberger A., Lee-Prudhoe J., Wood W.G., Higgs D.R., Iborra F.J., and Buckle V.J. Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172 (2006) 177-187
44. Lawrence J.B., and Clemson C.M. Gene associations: true romance or chance meeting in a nuclear neighborhood?. J Cell Biol 182 (2008) 1035-1038
45. Osborne C.S., Chakalova L., Brown K.E., Carter D., Horton A., Debrand E., Goyenechea B., Mitchell J.A., Lopes S., Reik W., et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36 (2004) 1065-1071
46. Chuang C.H., Carpenter A.E., Fuchsova B., Johnson T., de Lanerolle P., and Belmont A.S. Long-range directional movement of an interphase chromosome site. Curr Biol 16 (2006) 825-831
47. Dundr M., Ospina J.K., Sung M.H., John S., Upender M., Ried T., Hager G.L., and Matera A.G. Actin-dependent intranuclear repositioning of an active gene locus in vivo. J Cell Biol 179 (2007) 1095-1103
48. Ishii K., Arib G., Lin C., Van Houwe G., and Laemmli U.K. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 109 (2002) 551-562