Kaiser, T. E., Intine, R. V. & Dundr, M. De novo formation of a subnuclear body. Science322, 1713–1717 (2008). ArticleADSCAS Google Scholar
McStay, B. & Grummt, I. The epigenetics of rRNA genes: from molecular to chromosome biology. Annu. Rev. Cell Dev. Biol.24, 131–157 (2008). ArticleCAS Google Scholar
Lanctot, C., Cheutin, T., Cremer, M., Cavalli, G. & Cremer, T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nature Rev. Genet.8, 104–115 (2007). ArticleCAS Google Scholar
Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature453, 948–951 (2008). ArticleADSCAS Google Scholar
Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nature Genet.36, 1065–1071 (2004). ArticleCAS Google Scholar
Jackson, D. A., Hassan, A. B., Errington, R. J. & Cook, P. R. Visualization of focal sites of transcription within human nuclei. EMBO J.12, 1059–1065 (1993). ArticleCAS Google Scholar
Faro-Trindade, I. & Cook, P. R. Transcription factories: structures conserved during differentiation and evolution. Biochem. Soc. Trans.34, 1133–1137 (2006). ArticleCAS Google Scholar
Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature447, 413–417 (2007). ArticleADSCAS Google Scholar
Hassan, A. B. & Cook, P. R. Visualization of replication sites in unfixed human cells. J. Cell Sci.105, 541–550 (1993). PubMed Google Scholar
Chakalova, L., Debrand, E., Mitchell, J. A., Osborne, C. S. & Fraser, P. Replication and transcription: shaping the landscape of the genome. Nature Rev. Genet.6, 669–677 (2005). ArticleCAS Google Scholar
Göndör, A. & Ohlsson, R. Replication timing and epigenetic reprogramming of gene expression: a two-way relationship? Nature Rev. Genet.10, 269–276 (2009). Article Google Scholar
Soutoglou, E. & Misteli, T. Mobility and immobility of chromatin in transcription and genome stability. Curr. Opin. Genet. Dev.17, 435–442 (2007). ArticleCAS Google Scholar
Dostie, J. et al. Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res.16, 1299–1309 (2006). ArticleCAS Google Scholar
Rippe, K. Making contacts on a nucleic acid polymer. Trends Biochem. Sci.26, 733–740 (2001). ArticleCAS Google Scholar
Li, Q., Barkess, G. & Qian, H. Chromatin looping and the probability of transcription. Trends Genet.22, 197–202 (2006). Article Google Scholar
Ishihara, K., Oshimura, M. & Nakao, M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol. Cell23, 733–742 (2006). ArticleCAS Google Scholar
Cremer, T. & Cremer, C. Rise, fall and resurrection of chromosome territories: a historical perspective. Part II. Fall and resurrection of chromosome territories during the 1950s to 1980s. Part III. Chromosome territories and the functional nuclear architecture: experiments and models from the 1990s to the present. Eur. J. Histochem.50, 223–272 (2006). CASPubMed Google Scholar
Hu, Q. et al. Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc. Natl Acad. Sci. USA105, 19199–19204 (2008). This report demonstrates that chromatin crosstalk involves directed rapid movement of interacting loci and that this process is frequently accompanied by reorganization of the chromosome territories. ArticleADSCAS Google Scholar
Apostolou, E. & Thanos, D. Virus infection induces NF-κB-dependent interchromosomal associations mediating monoallelic IFN-β gene expression. Cell134, 85–96 (2008). This report shows that the organization of theIFNBenhanceosome requires the juxtaposition of one or more sequences from other chromosomes that contain NF-κB-bound Alu repeats. ArticleCAS Google Scholar
Walter, J., Hutter, B., Khare, T. & Paulsen, M. Repetitive elements in imprinted genes. Cytogenet. Genome Res.113, 109–115 (2006). ArticleCAS Google Scholar
Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genet.38, 1341–1347 (2006). ArticleCAS Google Scholar
Bartlett, J. et al. Specialized transcription factories. Biochem. Soc. Symp.73, 67–75 (2006). ArticleCAS Google Scholar
Xu, M. & Cook, P. R. Similar active genes cluster in specialized transcription factories. J. Cell Biol.181, 615–623 (2008). ArticleCAS Google Scholar
Cai, S., Lee, C. C. & Kohwi-Shigematsu, T. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nature Genet.38, 1278–1288 (2006). ArticleCAS Google Scholar
Vernimmen, D., De Gobbi, M., Sloane-Stanley, J. A., Wood, W. G. & Higgs, D. R. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J.26, 2041–2051 (2007). ArticleCAS Google Scholar
Tsytsykova, A. V. et al. Activation-dependent intrachromosomal interactions formed by the TNF gene promoter and two distal enhancers. Proc. Natl Acad. Sci. USA104, 16850–16855 (2007). ArticleADSCAS Google Scholar
Deschenes, J., Bourdeau, V., White, J. H. & Mader, S. Regulation of GREB1 transcription by estrogen receptor α through a multipartite enhancer spread over 20 kb of upstream flanking sequences. J. Biol. Chem.282, 17335–17339 (2007). ArticleCAS Google Scholar
Nemeth, A., Guibert, S., Tiwari, V. K., Ohlsson, R. & Langst, G. Epigenetic regulation of TTF-I-mediated promoter–terminator interactions of rRNA genes. EMBO J.27, 1255–1265 (2008). ArticleCAS Google Scholar
Bushey, A. M., Dorman, E. R. & Corces, V. G. Chromatin insulators: regulatory mechanisms and epigenetic inheritance. Mol. Cell32, 1–9 (2008). ArticleCAS Google Scholar
Ohlsson, R., Renkawitz, R. & Lobanenkov, V. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet.17, 520–527 (2001). ArticleCAS Google Scholar
Kim, J. H. et al. Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing. Genome Res.19, 533–544 (2009). ArticleCAS Google Scholar
Kim, T. H. et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell128, 1231–1245 (2007). ArticleCAS Google Scholar
Yusufzai, T. M., Tagami, H., Nakatani, Y. & Felsenfeld, G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol. Cell13, 291–298 (2004). ArticleCAS Google Scholar
Dekker, J. The three 'C's of chromosome conformation capture: controls, controls, controls. Nature Methods3, 17–21 (2006). ArticleCAS Google Scholar
Splinter, E. et al. CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus. Genes Dev.20, 2349–2354 (2006). ArticleCAS Google Scholar
Kurukuti, S. et al. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2 . Proc. Natl Acad. Sci. USA103, 10684–10689 (2006). ArticleADSCAS Google Scholar
Li, T. et al. CTCF regulates allelic expression of Igf2 by orchestrating a promoter-polycomb repressive complex 2 intrachromosomal loop. Mol. Cell. Biol.28, 6473–6482 (2008). ArticleCAS Google Scholar
Parelho, V. et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell132, 422–433 (2008). ArticleCAS Google Scholar
Wendt, K. S. et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature451, 796–801 (2008). ArticleADSCAS Google Scholar
Stedman, W. et al. Cohesins localize with CTCF at the KSHV latency control region and at cellular c-myc and H19/Igf2 insulators. EMBO J.27, 654–666 (2008). ArticleCAS Google Scholar
Hadjur, S. et al. Cohesins form chromosomal _cis_-interactions at the developmentally regulated IFNG locus. Nature460, 410–413 (2009). ArticleADSCAS Google Scholar
Göndör, A. & Ohlsson, R. Chromatin insulators and cohesins. EMBO Rep.9, 327–329 (2008). Article Google Scholar
Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet.38, 1348–1354 (2006). ArticleCAS Google Scholar
Ling, J. Q. et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1 . Science312, 269–272 (2006). ArticleADSCAS Google Scholar
Masui, O. & Heard, E. RNA and protein actors in X-chromosome inactivation. Cold Spring Harb. Symp. Quant. Biol.71, 419–428 (2006). ArticleCAS Google Scholar
Xu, N., Donohoe, M. E., Silva, S. S. & Lee, J. T. Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nature Genet.39, 1390–1396 (2007). ArticleCAS Google Scholar
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.20, 2223–2237 (2006). ArticleCAS Google Scholar
Zhao, J., Sun, B. K., Erwin, J. A., Song, J. J. & Lee, J. T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science322, 750–756 (2008). ArticleADSCAS Google Scholar
Lanzuolo, C., Roure, V., Dekker, J., Bantignies, F. & Orlando, V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nature Cell Biol.9, 1167–1174 (2007). ArticleCAS Google Scholar
Tiwari, V. K. et al. PcG proteins, DNA methylation, and gene repression by chromatin looping. PLoS Biol.6, e306 (2008). Article Google Scholar
Garrick, D. et al. The role of the polycomb complex in silencing α-globin gene expression in nonerythroid cells. Blood112, 3889–3899 (2008). ArticleCAS Google Scholar
Brown, J. M. et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J. Cell Biol.182, 1083–1097 (2008). ArticleCAS Google Scholar
Solovei, I. et al. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell137, 356–368 (2009). This report demonstrates that, contrary to expectations, the nuclear architecture in the rod cells of the eye can undergo dramatic reorganization to adapt to a new function associated with nocturnal mammals. ArticleCAS Google Scholar
Richter, K., Nessling, M. & Lichter, P. Macromolecular crowding and its potential impact on nuclear function. Biochim. Biophys. Acta1783, 2100–2107 (2008). ArticleCAS Google Scholar
Shimi, T. et al. The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes Dev.22, 3409–3421 (2008). ArticleCAS Google Scholar
Mehta, I. S., Elcock, L. S., Amira, M., Kill, I. R. & Bridger, J. M. Nuclear motors and nuclear structures containing A-type lamins and emerin: is there a functional link? Biochem. Soc. Trans.36, 1384–1388 (2008). ArticleCAS Google Scholar
Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R. & Flavell, R. A. Interchromosomal associations between alternatively expressed loci. Nature435, 637–645 (2005). ArticleADSCAS Google Scholar
Aladjem, M. I. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nature Rev. Genet.8, 588–600 (2007). ArticleCAS Google Scholar
Hiratani, I. et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol.6, e245 (2008). Article Google Scholar
Unneberg, P. & Claverie, J. M. Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST & mRNA data. PLoS ONE2, e254 (2007). ArticleADS Google Scholar
Ohlsson, R. Widespread monoallelic expression. Science318, 1077–1078 (2007). ArticleCAS Google Scholar
Parada, L. A., McQueen, P. G. & Misteli, T. Tissue-specific spatial organization of genomes. Genome Biol.5, R44 (2004). Article Google Scholar
Ghoussaini, M. et al. Multiple loci with different cancer specificities within the 8q24 gene desert. J. Natl Cancer Inst.100, 962–966 (2008). ArticleCAS Google Scholar
Steidl, U. et al. A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia. J. Clin. Invest.117, 2611–2620 (2007). ArticleCAS Google Scholar
Branco, M. R. & Pombo, A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol.4, e138 (2006). Article Google Scholar
Osborne, C. S. et al. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh . PLoS Biol.5, e192 (2007). Article Google Scholar