Interchromosomal clustering of active genes at the nuclear pore complex

References

• Fraser P, Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature 2007; 447:413 - 7; http://dx.doi.org/10.1038/nature05916; PMID: 17522674
   PubMed Web of Science ®Google Scholar
• Cremer T, Cremer M, Dietzel S, Müller S, Solovei I, Fakan S. Chromosome territories--a functional nuclear landscape. Curr Opin Cell Biol 2006; 18:307 - 16; http://dx.doi.org/10.1016/j.ceb.2006.04.007; PMID: 16687245
   PubMed Web of Science ®Google Scholar
• Cavalli G. Chromosome kissing. Curr Opin Genet Dev 2007; 17:443 - 50; http://dx.doi.org/10.1016/j.gde.2007.08.013; PMID: 17933509
   PubMed Web of Science ®Google Scholar
• Takizawa T, Meaburn KJ, Misteli T. The meaning of gene positioning. Cell 2008; 135:9 - 13; http://dx.doi.org/10.1016/j.cell.2008.09.026; PMID: 18854147
   PubMed Web of Science ®Google Scholar
• Schoenfelder S, Clay I, Fraser P. The transcriptional interactome: gene expression in 3D. Curr Opin Genet Dev 2010; 20:127 - 33; http://dx.doi.org/10.1016/j.gde.2010.02.002; PMID: 20211559
   PubMed Web of Science ®Google Scholar
• Meaburn KJ, Gudla PR, Khan S, Lockett SJ, Misteli T. Disease-specific gene repositioning in breast cancer. J Cell Biol 2009; 187:801 - 12; http://dx.doi.org/10.1083/jcb.200909127; PMID: 19995938
   PubMed Web of Science ®Google Scholar
• Meaburn KJ, Misteli T. Locus-specific and activity-independent gene repositioning during early tumorigenesis. J Cell Biol 2008; 180:39 - 50; http://dx.doi.org/10.1083/jcb.200708204; PMID: 18195100
   PubMed Web of Science ®Google Scholar
• Thompson M, Haeusler RA, Good PD, Engelke DR. Nucleolar clustering of dispersed tRNA genes. Science 2003; 302:1399 - 401; http://dx.doi.org/10.1126/science.1089814; PMID: 14631041
   PubMed Web of Science ®Google Scholar
• Heun P, Laroche T, Shimada K, Furrer P, Gasser SM. Chromosome dynamics in the yeast interphase nucleus. Science 2001; 294:2181 - 6; http://dx.doi.org/10.1126/science.1065366; PMID: 11739961
   PubMed Web of Science ®Google Scholar
• Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, et al. A three-dimensional model of the yeast genome. Nature 2010; 465:363 - 7; http://dx.doi.org/10.1038/nature08973; PMID: 20436457
   PubMed Web of Science ®Google Scholar
• Gotta M, Laroche T, Formenton A, Maillet L, Scherthan H, Gasser SM. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J Cell Biol 1996; 134:1349 - 63; http://dx.doi.org/10.1083/jcb.134.6.1349; PMID: 8830766
   PubMed Web of Science ®Google Scholar
• Gehlen LR, Gruenert G, Jones MB, Rodley CD, Langowski J, O’Sullivan JM. Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions. Nucleus 2012; 3:370 - 83; http://dx.doi.org/10.4161/nucl.20971; PMID: 22688649
   PubMed Web of Science ®Google Scholar
• Mateos-Langerak J, Cavalli G. Polycomb group proteins and long-range gene regulation. Adv Genet 2008; 61:45 - 66; http://dx.doi.org/10.1016/S0065-2660(07)00002-8; PMID: 18282502
   PubMed Web of Science ®Google Scholar
• Bantignies F, Grimaud C, Lavrov S, Gabut M, Cavalli G. Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev 2003; 17:2406 - 20; http://dx.doi.org/10.1101/gad.269503; PMID: 14522946
   PubMed Web of Science ®Google Scholar
• Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 2010; 42:53 - 61; http://dx.doi.org/10.1038/ng.496; PMID: 20010836
   PubMed Web of Science ®Google Scholar
• Eskiw CH, Cope NF, Clay I, Schoenfelder S, Nagano T, Fraser P. Transcription factories and nuclear organization of the genome. Cold Spring Harb Symp Quant Biol 2010; 75:501 - 6; http://dx.doi.org/10.1101/sqb.2010.75.046; PMID: 21467135
   PubMedGoogle Scholar
• Carter DR, Eskiw C, Cook PR. Transcription factories. Biochem Soc Trans 2008; 36:585 - 9; http://dx.doi.org/10.1042/BST0360585; PMID: 18631121
   PubMed Web of Science ®Google Scholar
• Xu M, Cook PR. The role of specialized transcription factories in chromosome pairing. Biochim Biophys Acta 2008; 1783:2155 - 60; http://dx.doi.org/10.1016/j.bbamcr.2008.07.013; PMID: 18706455
   PubMed Web of Science ®Google Scholar
• Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 2004; 117:427 - 39; http://dx.doi.org/10.1016/S0092-8674(04)00448-9; PMID: 15137937
   PubMed Web of Science ®Google Scholar
• Brickner JH, Walter P. Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2004; 2:e342; http://dx.doi.org/10.1371/journal.pbio.0020342; PMID: 15455074
   PubMed Web of Science ®Google Scholar
• Casolari JM, Brown CR, Drubin DA, Rando OJ, Silver PA. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev 2005; 19:1188 - 98; http://dx.doi.org/10.1101/gad.1307205; PMID: 15905407
   PubMed Web of Science ®Google Scholar
• Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer MW. Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 2010; 140:372 - 83; http://dx.doi.org/10.1016/j.cell.2009.12.054; PMID: 20144761
   PubMed Web of Science ®Google Scholar
• Kalverda B, Pickersgill H, Shloma VV, Fornerod M. Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 2010; 140:360 - 71; http://dx.doi.org/10.1016/j.cell.2010.01.011; PMID: 20144760
   PubMed Web of Science ®Google Scholar
• Brickner DG, Cajigas I, Fondufe-Mittendorf Y, Ahmed S, Lee PC, Widom J, et al. H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol 2007; 5:e81; http://dx.doi.org/10.1371/journal.pbio.0050081; PMID: 17373856
   PubMed Web of Science ®Google Scholar
• Ahmed S, Brickner DG, Light WH, Cajigas I, McDonough M, Froyshteter AB, et al. DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery. Nat Cell Biol 2010; 12:111 - 8; http://dx.doi.org/10.1038/ncb2011; PMID: 20098417
   PubMed Web of Science ®Google Scholar
• Cabal GG, Genovesio A, Rodriguez-Navarro S, Zimmer C, Gadal O, Lesne A, et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 2006; 441:770 - 3; http://dx.doi.org/10.1038/nature04752; PMID: 16760982
   PubMed Web of Science ®Google Scholar
• Luthra R, Kerr SC, Harreman MT, Apponi LH, Fasken MB, Ramineni S, et al. Actively transcribed GAL genes can be physically linked to the nuclear pore by the SAGA chromatin modifying complex. J Biol Chem 2007; 282:3042 - 9; http://dx.doi.org/10.1074/jbc.M608741200; PMID: 17158105
   PubMed Web of Science ®Google Scholar
• Dieppois G, Iglesias N, Stutz F. Cotranscriptional recruitment to the mRNA export receptor Mex67p contributes to nuclear pore anchoring of activated genes. Mol Cell Biol 2006; 26:7858 - 70; http://dx.doi.org/10.1128/MCB.00870-06; PMID: 16954382
   PubMed Web of Science ®Google Scholar
• Schmid M, Arib G, Laemmli C, Nishikawa J, Durussel T, Laemmli UK. Nup-PI: the nucleopore-promoter interaction of genes in yeast. Mol Cell 2006; 21:379 - 91; http://dx.doi.org/10.1016/j.molcel.2005.12.012; PMID: 16455493
   PubMed Web of Science ®Google Scholar
• Light WH, Brickner DG, Brand VR, Brickner JH. Interaction of a DNA zip code with the nuclear pore complex promotes H2A.Z incorporation and INO1 transcriptional memory. Mol Cell 2010; 40:112 - 25; http://dx.doi.org/10.1016/j.molcel.2010.09.007; PMID: 20932479
   PubMed Web of Science ®Google Scholar
• Brickner DG, Ahmed S, Meldi L, Thompson A, Light W, Young M, et al. Transcription factor binding to a DNA zip code controls interchromosomal clustering at the nuclear periphery. Dev Cell 2012; 22:1234 - 46; http://dx.doi.org/10.1016/j.devcel.2012.03.012; PMID: 22579222
   PubMed Web of Science ®Google Scholar
• Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, et al. The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control. J Cell Biol 2005; 171:955 - 65; http://dx.doi.org/10.1083/jcb.200509061; PMID: 16365162
   PubMed Web of Science ®Google Scholar
• Ishii K, Arib G, Lin C, Van Houwe G, Laemmli UK. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 2002; 109:551 - 62; http://dx.doi.org/10.1016/S0092-8674(02)00756-0; PMID: 12062099
   PubMed Web of Science ®Google Scholar
• Kalverda B, Fornerod M. Characterization of genome-nucleoporin interactions in Drosophila links chromatin insulators to the nuclear pore complex. Cell Cycle 2010; 9:4812 - 7; http://dx.doi.org/10.4161/cc.9.24.14328; PMID: 21150273
   PubMed Web of Science ®Google Scholar
• Tan-Wong SM, Wijayatilake HD, Proudfoot NJ. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev 2009; 23:2610 - 24; http://dx.doi.org/10.1101/gad.1823209; PMID: 19933151
   PubMed Web of Science ®Google Scholar
• Green EM, Jiang Y, Joyner R, Weis K. A negative feedback loop at the nuclear periphery regulates GAL gene expression. Mol Biol Cell 2012; 23:1367 - 75; http://dx.doi.org/10.1091/mbc.E11-06-0547; PMID: 22323286
   PubMed Web of Science ®Google Scholar
• Berger AB, Cabal GG, Fabre E, Duong T, Buc H, Nehrbass U, et al. High-resolution statistical mapping reveals gene territories in live yeast. Nat Methods 2008; 5:1031 - 7; http://dx.doi.org/10.1038/nmeth.1266; PMID: 18978785
   PubMed Web of Science ®Google Scholar
• Gard S, Light W, Xiong B, Bose T, McNairn AJ, Harris B, et al. Cohesinopathy mutations disrupt the subnuclear organization of chromatin. J Cell Biol 2009; 187:455 - 62; http://dx.doi.org/10.1083/jcb.200906075; PMID: 19948494
   PubMed Web of Science ®Google Scholar
• Brickner DG, Brickner JH. Cdk phosphorylation of a nucleoporin controls localization of active genes through the cell cycle. Mol Biol Cell 2010; 21:3421 - 32; http://dx.doi.org/10.1091/mbc.E10-01-0065; PMID: 20702586
   PubMed Web of Science ®Google Scholar
• Siddiqui AH, Brandriss MC. The Saccharomyces cerevisiae PUT3 activator protein associates with proline-specific upstream activation sequences. Mol Cell Biol 1989; 9:4706 - 12; PMID: 2689862
   PubMed Web of Science ®Google Scholar
• Kosak ST, Skok JA, Medina KL, Riblet R, Le Beau MM, Fisher AG, et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 2002; 296:158 - 62; http://dx.doi.org/10.1126/science.1068768; PMID: 11935030
   PubMed Web of Science ®Google Scholar
• Takizawa T, Gudla PR, Guo L, Lockett S, Misteli T. Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. Genes Dev 2008; 22:489 - 98; http://dx.doi.org/10.1101/gad.1634608; PMID: 18281462
   PubMed Web of Science ®Google Scholar
• Zink D, Amaral MD, Englmann A, Lang S, Clarke LA, Rudolph C, et al. Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 2004; 166:815 - 25; http://dx.doi.org/10.1083/jcb.200404107; PMID: 15364959
   PubMed Web of Science ®Google Scholar
• Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B, Bonnet J, et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 2011; 144:214 - 26; http://dx.doi.org/10.1016/j.cell.2010.12.026; PMID: 21241892
   PubMed Web of Science ®Google Scholar
• Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, et al. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 2012; 149:1474 - 87; http://dx.doi.org/10.1016/j.cell.2012.04.035; PMID: 22726435
   PubMed Web of Science ®Google Scholar
• Vazquez J, Müller M, Pirrotta V, Sedat JW. The Mcp element mediates stable long-range chromosome-chromosome interactions in Drosophila. Mol Biol Cell 2006; 17:2158 - 65; http://dx.doi.org/10.1091/mbc.E06-01-0049; PMID: 16495335
   PubMed Web of Science ®Google Scholar
• Capelson M, Hetzer MW. The role of nuclear pores in gene regulation, development and disease. EMBO Rep 2009; 10:697 - 705; http://dx.doi.org/10.1038/embor.2009.147; PMID: 19543230
   PubMed Web of Science ®Google Scholar
• Brown CR, Kennedy CJ, Delmar VA, Forbes DJ, Silver PA. Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. Genes Dev 2008; 22:627 - 39; http://dx.doi.org/10.1101/gad.1632708; PMID: 18316479
   PubMed Web of Science ®Google Scholar
• Shevtsov SP, Dundr M. Nucleation of nuclear bodies by RNA. Nat Cell Biol 2011; 13:167 - 73; http://dx.doi.org/10.1038/ncb2157; PMID: 21240286
   PubMed Web of Science ®Google Scholar
• Kaiser TE, Intine RV, Dundr M. De novo formation of a subnuclear body. Science 2008; 322:1713 - 7; http://dx.doi.org/10.1126/science.1165216; PMID: 18948503
   PubMed Web of Science ®Google Scholar
• Mao YS, Sunwoo H, Zhang B, Spector DL. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol 2011; 13:95 - 101; http://dx.doi.org/10.1038/ncb2140; PMID: 21170033
   PubMed Web of Science ®Google Scholar
• Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, et al. Global analysis of protein localization in budding yeast. Nature 2003; 425:686 - 91; http://dx.doi.org/10.1038/nature02026; PMID: 14562095
   PubMed Web of Science ®Google Scholar
• Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM. The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion. Genome Res 2009; 19:611 - 25; http://dx.doi.org/10.1101/gr.083881.108; PMID: 19179643
   PubMed Web of Science ®Google Scholar