Chromosome organization in the nucleus - charting new territory across the Hi-Cs

Current Opinion in Genetics and Development

Volumn 22, Issue 2, 2012, Pages 125-131

  Dostie, Josée ^a   Bickmore, Wendy A ^b  

^a MCGILL UNIVERSITY   (Canada)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS; CENTROMERE; CENTROSOME; CHROMATIN STRUCTURE; CHROMOSOME STRUCTURE; CHROMOSOME TERRITORY ORGANIZATION; CONFORMATION; DNA DENATURATION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CONTROL; GENE EXPRESSION REGULATION; GENE LOCUS; GENOMICS; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; TRANSCRIPTION REGULATION; X CHROMOSOME INACTIVATION;

ANIMALS; CELL NUCLEUS; CHROMOSOMES; GENE EXPRESSION REGULATION; GENETIC TECHNIQUES; HUMANS;

EID: 84860380106     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2011.12.006     Document Type: Review

References (49)

1. Solovei I., Kreysing M., Lanctôt C., Kösem S., Peichl L., Cremer T., Guck J., Joffe B. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 2009, 137:356-368.
2. Joffe B., Leonhardt H., Solovei I. Differentiation and large scale spatial organization of the genome. Curr Opin Genet Dev 2010, 20:562-569.
3. Deniaud E., Bickmore W.A. Transcription and the nuclear periphery: edge of darkness?. Curr Opin Genet Dev 2009, 19:187-191.
4. Gilbert N., Boyle S., Fiegler H., Woodfine K., Carter N.P., Bickmore W.A. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 2004, 118:555-566.
5. Morey C., Da Silva N.R., Perry P., Bickmore W.A. Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 2007, 134:909-919.
6. van Steensel B., Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol 2010, 28:1089-1095.
7. Simonis M., Kooren J., de Laat W. An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 2007, 4:895-901.
8. Xu Z., Wei G., Chepelev I., Zhao K., Felsenfeld G. Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription. Nat Struct Mol Biol 2011, 18:372-378.
9. Montavon T., Soshnikova N., Mascrez B., Joye E., Thevenet L., Splinter E., de Laat W., Spitz F., Duboule D. A regulatory archipelago controls hox genes transcription in digits. Cell 2011, 147:1132-1145.
10. Splinter E., de Wit E., Nora E.P., Klous P., van de Werken H.J.G., Zhu Y., Kaaij L.J.T., van Ijcken W., Gribnau J., Heard E., et al. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev 2011, 25:1371-1383.
11. 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.
12. Tolhuis B., Blom M., Kerkhoven R.M., Pagie L., Teunissen H., Nieuwland M., Simonis M., de Laat W., van Lohuizen M., van Steensel B. Interactions among polycomb domains are guided by chromosome architecture. PLoS Genet 2011, 7:e1001343.
13. Hakim O., Sung M.-H., Voss T.C., Splinter E., John S., Sabo P.J., Thurman R.E., Stamatoyannopoulos J.A., de Laat W., Hager G.L. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res 2011, 21:697-706.
14. 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 2006, 16:1299-1309.
15. Fraser J., Rousseau M., Shenker S., Ferraiuolo M.A., Hayashizaki Y., Blanchette M., Dostie J. Chromatin conformation signatures of cellular differentiation. Genome Biol 2009, 10:R37.
16. Baù D., Sanyal A., Lajoie B.R., Capriotti E., Byron M., Lawrence J.B., Dekker J., Marti-Renom M.A. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol 2011, 18:107-114.
17. 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.
18. Fullwood M.J., Liu M.H., Pan Y.F., Liu J., Xu H., Mohamed Y.B., Orlov Y.L., Velkov S., Ho A., Mei P.H., et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009, 462:58-64.
19. Yaffe E., Tanay A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 2011, 43:1059-1065.
20. Duan Z., Andronescu M., Schutz K., McIlwain S., Kim Y.J., Lee C., Shendure J., Fields S., Blau C.A., Noble W.S. A three-dimensional model of the yeast genome. Nature 2010, 465:363-367.
21. Handoko L., Xu H., Li G., Ngan C.Y., Chew E., Schnapp M., Lee C.W.H., Ye C., Ping J.L.H., Mulawadi F., et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011, 43:630-638.
22. Morey C., Avner P. The demoiselle of x-inactivation: 50 years old and as trendy and mesmerising as ever. PLoS Genet 2011, 7:e1002212.
23. Clemson C.M., McNeil J.A., Willard H.F., Lawrence J.B. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 1996, 132:259-275.
24. Clemson C.M., Hall L.L., Byron M., McNeil J., Lawrence J.B. The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc Natl Acad Sci USA 2006, 103:7688-7693.
25. Popova B.C., Tada T., Takagi N., Brockdorff N., Nesterova T.B. Attenuated spread of X-inactivation in an X;autosome translocation. Proc Natl Acad Sci USA 2006, 103:7706-7711.
26. Chaumeil J., Le Baccon P., Wutz A., Heard E. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev 2006, 20:2223-2237.
27. Rego A., Sinclair P.B., Tao W., Kireev I., Belmont A.S. The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure. J Cell Sci 2008, 121:1119-1127.
28. Teller K., Illner D., Thamm S., Casas-Delucchi C.S., Versteeg R., Indemans M., Cremer T., Cremer M. A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at ≥ 20Mb genomic length scales. Nucleus 2011, 2:465-477.
29. Grimaud C., Becker P.B. The dosage compensation complex shapes the conformation of the X chromosome in Drosophila. Genes Dev 2009, 23:2490-2495.
30. Morey C., Kress C., Bickmore W.A. Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression. Genome Res 2009, 19:1184-1194.
31. Mahy N.L., Perry P.E., Bickmore W.A. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 2002, 159:753-763.
32. Boyle S., Rodesch M.J., Halvensleben H.A., Jeddeloh J.A., Bickmore W.A. Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosome Res 2011, 19:901-909.
33. 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.
34. Dietzel S., Jauch A., Kienle D., Qu G., Holtgreve-Grez H., Eils R., Münkel C., Bittner M., Meltzer P.S., Trent J.M., et al. Separate and variably shaped chromosome arm domains are disclosed by chromosome arm painting in human cell nuclei. Chromosome Res 1998, 6:25-33.
35. Bantignies F., Roure V., Comet I., Leblanc B., Schuettengruber B., Bonnet J., Tixier V., Mas A., Cavalli G. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 2011, 144:214-226.
36. Noonan J.P., McCallion A.S. Genomics of long-range regulatory elements. Annu Rev Genomics Hum Genet 2010, 11:1-23.
37. Brown J.M., Leach J., Reittie J.E., Atzberger A., Lee-Prudhoe J., Wood W.G., Higgs D.R., Iborra F.J., Buckle V.J. Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 2006, 172:177-187.
38. Brown J.M., Green J., Neves das R.P., Wallace H.A.C., Smith A.J.H., 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 2008, 182:1083-1097.
39. Eskeland R., Leeb M., Grimes G.R., Kress C., Boyle S., Sproul D., Gilbert N., Fan Y., Skoultchi A.I., Wutz A., et al. Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell 2010, 38:452-464.
40. Ferraiuolo M.A., Rousseau M., Miyamoto C., Shenker S., Wang X.Q.D., Nadler M., Blanchette M., Dostie J. The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res 2010, 38:7472-7484.
41. Noordermeer D., Leleu M., Splinter E., Rougemont J., de Laat W., Duboule D. The dynamic architecture of Hox gene clusters. Science 2011, 334:222-225.
42. Wang K.C., Yang Y.W., Liu B., Sanyal A., Corces-Zimmerman R., Chen Y., Lajoie B.R., Protacio A., Flynn R.A., Gupta R.A., et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011, 472:120-124.
43. 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.
44. Marchetti M., Fanti L., Berloco M., Pimpinelli S. Differential expression of the Drosophila BX-C in polytene chromosomes in cells of larval fat bodies: a cytological approach to identifying in vivo targets of the homeotic Ubx, Abd-A and Abd-B proteins. Development 2003, 130:3683-3689.
45. Sutherland H., Bickmore W.A. Transcription factories: gene expression in unions?. Nat Rev Genet 2009, 10:457-466.
46. Baù D., Marti-Renom M.A. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res 2011, 19:25-35.
47. Müller I., Boyle S., Singer R.H., Bickmore W.A., Chubb J.R. Stable morphology, but dynamic internal reorganisation, of interphase human chromosomes in living cells. PLoS ONE 2010, 5:e11560.
48. Masui O., Bonnet I., Le Baccon P., Brito I., Pollex T., Murphy N., Hupé P., Barillot E., Belmont A.S., Heard E. Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell 2011, 145:447-458.
49. McNally J.G. Foreword. Biophysics in chromatin structure and nuclear dynamics. Chromosome Res 2011, 19:1-3.