Are genes switched on when they kiss?

References

• Kioussis D. Gene regulation: kissing chromosomes. Nature 2005; 435:579 - 80; http://dx.doi.org/10.1038/435579a; PMID: 15931207
   PubMed Web of Science ®Google Scholar
• Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 2004; 36:1065 - 71; http://dx.doi.org/10.1038/ng1423; PMID: 15361872
   PubMed Web of Science ®Google Scholar
• Noordermeer D, de Wit E, Klous P, van de Werken H, Simonis M, Lopez-Jones M, Eussen B, de Klein A, Singer RH, de Laat W. Variegated gene expression caused by cell-specific long-range DNA interactions. Nat Cell Biol 2011; 13:944 - 51; http://dx.doi.org/10.1038/ncb2278; PMID: 21706023
   PubMedGoogle Scholar
• Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR. Active RNA polymerases: mobile or immobile molecular machines?. PLoS Biol 2010; 8:e1000419; http://dx.doi.org/10.1371/journal.pbio.1000419; PMID: 20644712
   PubMed Web of Science ®Google Scholar
• Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, 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
• Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 2012; 148:84 - 98; http://dx.doi.org/10.1016/j.cell.2011.12.014; PMID: 22265404
   PubMed Web of Science ®Google Scholar
• Sandhu KS, Li G, Poh HM, Quek YL, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, et al. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep 2012; 2:1207 - 19; http://dx.doi.org/10.1016/j.celrep.2012.09.022; PMID: 23103170
   PubMed Web of Science ®Google Scholar
• Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell 2013; 49:773 - 82; http://dx.doi.org/10.1016/j.molcel.2013.02.011; PMID: 23473598
   PubMed Web of Science ®Google Scholar
• Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002; 295:1306 - 11; http://dx.doi.org/10.1126/science.1067799; PMID: 11847345
   PubMed Web of Science ®Google Scholar
• Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009; 462:58 - 64; http://dx.doi.org/10.1038/nature08497; PMID: 19890323
   PubMed Web of Science ®Google Scholar
• 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 - 54; http://dx.doi.org/10.1038/ng1896; PMID: 17033623
   PubMed Web of Science ®Google Scholar
• Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature 2012; 489:109 - 13; http://dx.doi.org/10.1038/nature11279; PMID: 22955621
   PubMed Web of Science ®Google Scholar
• Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 2013; 504:306 - 10; http://dx.doi.org/10.1038/nature12716; PMID: 24213634
   PubMed Web of Science ®Google Scholar
• Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 2012; 149:1233 - 44; http://dx.doi.org/10.1016/j.cell.2012.03.051; PMID: 22682246
   PubMed Web of Science ®Google Scholar
• Vernimmen D, De Gobbi M, Sloane-Stanley JA, Wood WG, Higgs DR. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J 2007; 26:2041 - 51; http://dx.doi.org/10.1038/sj.emboj.7601654; PMID: 17380126
   PubMed Web of Science ®Google Scholar
• Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res 2010; 38:4325 - 36; http://dx.doi.org/10.1093/nar/gkq175; PMID: 20360044
   PubMed Web of Science ®Google Scholar
• Wright JB, Brown SJ, Cole MD. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol 2010; 30:1411 - 20; http://dx.doi.org/10.1128/MCB.01384-09; PMID: 20065031
   PubMed Web of Science ®Google Scholar
• Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 2013; 503:290 - 4; PMID: 24141950
   PubMed Web of Science ®Google Scholar
• Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Léveillé N, Kalluri R, et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 2013; 49:524 - 35; http://dx.doi.org/10.1016/j.molcel.2012.11.021; PMID: 23273978
   PubMed Web of Science ®Google Scholar
• Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 2013; 153:1281 - 95; http://dx.doi.org/10.1016/j.cell.2013.04.053; PMID: 23706625
   PubMed Web of Science ®Google Scholar
• Cremer T, Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol 2010; 2:a003889; http://dx.doi.org/10.1101/cshperspect.a003889; PMID: 20300217
   PubMed Web of Science ®Google Scholar
• Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA. Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 1999; 145:1119 - 31; http://dx.doi.org/10.1083/jcb.145.6.1119; PMID: 10366586
   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
• Branco MR, Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 2006; 4:e138; http://dx.doi.org/10.1371/journal.pbio.0040138; PMID: 16623600
   PubMed Web of Science ®Google Scholar
• Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009; 326:289 - 93; http://dx.doi.org/10.1126/science.1181369; PMID: 19815776
   PubMed Web of Science ®Google Scholar
• Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012; 485:376 - 80; http://dx.doi.org/10.1038/nature11082; PMID: 22495300
   PubMed Web of Science ®Google Scholar
• Cook PR. The organization of replication and transcription. Science 1999; 284:1790 - 5; http://dx.doi.org/10.1126/science.284.5421.1790; PMID: 10364545
   PubMed Web of Science ®Google Scholar
• Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA. Interchromosomal associations between alternatively expressed loci. Nature 2005; 435:637 - 45; http://dx.doi.org/10.1038/nature03574; PMID: 15880101
   PubMed Web of Science ®Google Scholar
• Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The dynamic architecture of Hox gene clusters. Science 2011; 334:222 - 5; http://dx.doi.org/10.1126/science.1207194; PMID: 21998387
   PubMed Web of Science ®Google Scholar
• Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, et al. TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J 2012; 31:4404 - 14; http://dx.doi.org/10.1038/emboj.2012.288; PMID: 23103767
   PubMed Web of Science ®Google Scholar
• Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012; 485:381 - 5; http://dx.doi.org/10.1038/nature11049; PMID: 22495304
   PubMed Web of Science ®Google Scholar
• Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 2013; 502:59 - 64; http://dx.doi.org/10.1038/nature12593; PMID: 24067610
   PubMed Web of Science ®Google Scholar
• Apostolou E, Thanos D. Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell 2008; 134:85 - 96; http://dx.doi.org/10.1016/j.cell.2008.05.052; PMID: 18614013
   PubMed Web of Science ®Google Scholar
• Wada Y, Ohta Y, Xu M, Tsutsumi S, Minami T, Inoue K, Komura D, Kitakami J, Oshida N, Papantonis A, et al. A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A 2009; 106:18357 - 61; http://dx.doi.org/10.1073/pnas.0902573106; PMID: 19826084
   PubMed Web of Science ®Google Scholar
• Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 1996; 93:1156 - 60; http://dx.doi.org/10.1073/pnas.93.3.1156; PMID: 8577732
   PubMed Web of Science ®Google Scholar
• Bibikova M, Beumer K, Trautman JK, Carroll D. Enhancing gene targeting with designed zinc finger nucleases. Science 2003; 300:764; http://dx.doi.org/10.1126/science.1079512; PMID: 12730594
   PubMed Web of Science ®Google Scholar
• Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 2011; 39:359 - 72; http://dx.doi.org/10.1093/nar/gkq704; PMID: 20699274
   PubMed Web of Science ®Google Scholar
• Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012; 337:816 - 21; http://dx.doi.org/10.1126/science.1225829; PMID: 22745249
   PubMed Web of Science ®Google Scholar
• Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 2010; 186:757 - 61; http://dx.doi.org/10.1534/genetics.110.120717; PMID: 20660643
   PubMed Web of Science ®Google Scholar
• Li L, Wu LP, Chandrasegaran S. Functional domains in Fok I restriction endonuclease. Proc Natl Acad Sci U S A 1992; 89:4275 - 9; http://dx.doi.org/10.1073/pnas.89.10.4275; PMID: 1584761
   PubMedGoogle Scholar
• Li L, Wu LP, Clarke R, Chandrasegaran S. C-terminal deletion mutants of the FokI restriction endonuclease. Gene 1993; 133:79 - 84; http://dx.doi.org/10.1016/0378-1119(93)90227-T; PMID: 8224897
   PubMedGoogle Scholar
• Li L, Chandrasegaran S. Alteration of the cleavage distance of Fok I restriction endonuclease by insertion mutagenesis. Proc Natl Acad Sci U S A 1993; 90:2764 - 8; http://dx.doi.org/10.1073/pnas.90.7.2764; PMID: 8464886
   PubMedGoogle Scholar
• Kim YG, Li L, Chandrasegaran S. Insertion and deletion mutants of FokI restriction endonuclease. J Biol Chem 1994; 269:31978 - 82; PMID: 7989374
   PubMed Web of Science ®Google Scholar
• Smith J, Bibikova M, Whitby FG, Reddy AR, Chandrasegaran S, Carroll D. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 2000; 28:3361 - 9; http://dx.doi.org/10.1093/nar/28.17.3361; PMID: 10954606
   PubMed Web of Science ®Google Scholar
• Hoeijmakers JHJ. Genome maintenance mechanisms for preventing cancer. Nature 2001; 411:366 - 74; http://dx.doi.org/10.1038/35077232; PMID: 11357144
   PubMed Web of Science ®Google Scholar
• Fanucchi S, Shibayama Y, Burd S, Weinberg MS, Mhlanga MM. Chromosomal contact permits transcription between coregulated genes. Cell 2013; 155:606 - 20; http://dx.doi.org/10.1016/j.cell.2013.09.051; PMID: 24243018
   PubMed Web of Science ®Google Scholar
• Rogakou EP, Boon C, Redon C, Bonner WM. Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol 1999; 146:905 - 16; http://dx.doi.org/10.1083/jcb.146.5.905; PMID: 10477747
   PubMed Web of Science ®Google Scholar
• Kruhlak M, Crouch EE, Orlov M, Montaño C, Gorski SA, Nussenzweig A, Misteli T, Phair RD, Casellas R. The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks. Nature 2007; 447:730 - 4; http://dx.doi.org/10.1038/nature05842; PMID: 17554310
   PubMed Web of Science ®Google Scholar
• Shanbhag NM, Rafalska-Metcalf IU, Balane-Bolivar C, Janicki SM, Greenberg RA. ATM-dependent chromatin changes silence transcription in cis to DNA double-strand breaks. Cell 2010; 141:970 - 81; http://dx.doi.org/10.1016/j.cell.2010.04.038; PMID: 20550933
   PubMed Web of Science ®Google Scholar
• Dion V, Gasser SM. Chromatin movement in the maintenance of genome stability. Cell 2013; 152:1355 - 64; http://dx.doi.org/10.1016/j.cell.2013.02.010; PMID: 23498942
   PubMed Web of Science ®Google Scholar
• Larkin JD, Papantonis A, Cook PR. Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites. J Cell Sci 2013; 126:2052 - 9; http://dx.doi.org/10.1242/jcs.123653; PMID: 23444365
   PubMedGoogle Scholar
• Abney JR, Cutler B, Fillbach ML, Axelrod D, Scalettar BA. Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J Cell Biol 1997; 137:1459 - 68; http://dx.doi.org/10.1083/jcb.137.7.1459; PMID: 9199163
   PubMed Web of Science ®Google Scholar
• Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 1997; 7:930 - 9; http://dx.doi.org/10.1016/S0960-9822(06)00412-X; PMID: 9382846
   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
• Henriques R, Griffiths C, Hesper Rego E, Mhlanga MM. PALM and STORM: unlocking live-cell super-resolution. Biopolymers 2011; 95:322 - 31; http://dx.doi.org/10.1002/bip.21586; PMID: 21254001
   PubMed Web of Science ®Google Scholar
• Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, Dugast-Darzacq C, Hajj B, Dahan M, Darzacq X. Real-time dynamics of RNA polymerase II clustering in live human cells. Science 2013; 341:664 - 7; http://dx.doi.org/10.1126/science.1239053; PMID: 23828889
   PubMed Web of Science ®Google Scholar
• Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 2013; 155:1479 - 91; http://dx.doi.org/10.1016/j.cell.2013.12.001; PMID: 24360272
   PubMed Web of Science ®Google Scholar
• Miyanari Y, Ziegler-Birling C, Torres-Padilla ME. Live visualization of chromatin dynamics with fluorescent TALEs. Nat Struct Mol Biol 2013; 20:1321 - 4; http://dx.doi.org/10.1038/nsmb.2680; PMID: 24096363
   PubMed Web of Science ®Google Scholar
• Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 2013; 154:442 - 51; http://dx.doi.org/10.1016/j.cell.2013.06.044; PMID: 23849981
   PubMed Web of Science ®Google Scholar
• Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, 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 - 309; http://dx.doi.org/10.1101/gr.5571506; PMID: 16954542
   PubMed Web of Science ®Google Scholar
• Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet 2005; 37:31 - 40; PMID: 15608638
   PubMed Web of Science ®Google Scholar
• Langer-Safer PR, Levine M, Ward DC. Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Natl Acad Sci U S A 1982; 79:4381 - 5; http://dx.doi.org/10.1073/pnas.79.14.4381; PMID: 6812046
   PubMed Web of Science ®Google Scholar
• Bienko M, Crosetto N, Teytelman L, Klemm S, Itzkovitz S, van Oudenaarden A. A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat Methods 2013; 10:122 - 4; http://dx.doi.org/10.1038/nmeth.2306; PMID: 23263692
   PubMedGoogle Scholar
• Cremer T, Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol 2010; 2:a003889; http://dx.doi.org/10.1101/cshperspect.a003889; PMID: 20300217
   PubMed Web of Science ®Google Scholar
• Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 2008; 5:877 - 9; http://dx.doi.org/10.1038/nmeth.1253; PMID: 18806792
   PubMed Web of Science ®Google Scholar
• Levesque MJ, Raj A. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Nat Methods 2013; 10:246 - 8; http://dx.doi.org/10.1038/nmeth.2372; PMID: 23416756
   PubMed Web of Science ®Google Scholar
• Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013; 339:819 - 23; http://dx.doi.org/10.1126/science.1231143; PMID: 23287718
   PubMed Web of Science ®Google Scholar
• Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science 2013; 339:823 - 6; http://dx.doi.org/10.1126/science.1232033; PMID: 23287722
   PubMed Web of Science ®Google Scholar