Chromatin interaction networks and higher order architectures of eukaryotic genomes

Journal of Cellular Biochemistry

Volumn 112, Issue 9, 2011, Pages 2218-2221

  Singh Sandhu, Kuljeet ^a   Li, Guoliang ^a   Sung, Wing Kin ^a,b   Ruan, Yijun ^a,c  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Chromatin 3D architecture; Chromatin interaction; Genome; Interaction networks

Indexed keywords

ARTICLE; CHROMATIN; CHROMATIN INTERACTION NETWORK; CYTOARCHITECTURE; EPIGENETICS; EUKARYOTE; EUKARYOTIC GENOME; GENE REGULATORY NETWORK; GENOME; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROTEIN INTERACTION;

ANIMALS; CHROMATIN; EPIGENESIS, GENETIC; EPIGENOMICS; GENE REGULATORY NETWORKS; GENOME; HUMANS; MOLECULAR CONFORMATION;

EUKARYOTA;

EID: 84860395199     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.23155     Document Type: Article

References (27)

1. Albert R, Jeong H, Barabasi AL,. 2000. Error and attack tolerance of complex networks. Nature 406: 378-382. (Pubitemid 30625551)
2. Barabási A-L, Bonabeau E,. 2003. Scale-free networks. Sci Am 288: 60-69.
3. Barabasi AL, Oltvai ZN,. 2004. Network biology: Understanding the cell's functional organization. Nat Rev Genet 5: 101-113. (Pubitemid 38160277)
4. Buldyrev SV, Parshani R, Paul G, Stanley HE, Havlin S,. 2010. Catastrophic cascade of failures in interdependent networks. Nature 464: 1025-1028.
5. Davila Lopez M, Martinez Guerra JJ, Samuelsson T,. 2010. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PLoS One 5: e10654.
6. Dekker J, Rippe K, Dekker M, Kleckner N,. 2002. Capturing chromosome conformation. Science 295: 1306-1311. (Pubitemid 34157624)
7. Deschenes J, Bourdeau V, White JH, Mader S,. 2007. Regulation of GREB1 transcription by estrogen receptor alpha through a multipartite enhancer spread over 20kb of upstream flanking sequences. J Biol Chem 282: 17335-17339. (Pubitemid 47100267)
8. Dorier J, Stasiak A,. 2010. The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture. Nucleic Acids Res 38: 7410-7428
9. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J,. 2006. Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res 16: 1299-1309. (Pubitemid 44506963)
10. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS,. 2010. A three-dimensional model of the yeast genome. Nature 465: 363-367.
11. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y,. 2009. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462: 58-64.
12. Hurst LD, Pal C, Lercher MJ,. 2004. The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299-310. (Pubitemid 38435625)
13. Kitamura E, Blow JJ, Tanaka TU,. 2006. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell 125: 1297-1308. (Pubitemid 43929088)
14. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J,. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
15. Lin C, Yang L, Tanasa B, Hutt K, Ju BG, Ohgi K, Zhang J, Rose DW, Fu XD, Glass CK, Rosenfeld MG,. 2009. Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 139: 1069-1083.
16. Lisby M, Rothstein R, Mortensen UH,. 2001. Rad52 forms DNA repair and recombination centers during S phase. Proc Natl Acad Sci U S A 98: 8276-8282. (Pubitemid 32678024)
17. Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R,. 2006. Interchromosomal interactions and olfactory receptor choice. Cell 126: 403-413. (Pubitemid 44092961)
18. Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P,. 2004. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36: 1065-1071. (Pubitemid 41184467)
19. Parshani R, Buldyrev SV, Havlin S,. 2010. Interdependent networks: Reducing the coupling strength leads to a change from a first to second order percolation transition. Phys Rev Lett 105: 048701.
20. Sandhu KS, Shi C, Sjolinder M, Zhao Z, Gondor A, Liu L, Tiwari VK, Guibert S, Emilsson L, Imreh MP, Ohlsson R,. 2009. Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. Genes Dev 23: 2598-2603.
21. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei CL, Ruan Y, Bieker JJ, Fraser P,. 2009. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42: 53-61.
22. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W,. 2006. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38: 1348-1354. (Pubitemid 44646300)
23. Solovei I, Kreysing M, Lanctot C, Kosem S, Peichl L, Cremer T, Guck J, Joffe B,. 2009. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 137: 356-368.
24. Steidl U, Steidl C, Ebralidze A, Chapuy B, Han HJ, Will B, Rosenbauer F, Becker A, Wagner K, Koschmieder S, Kobayashi S, Costa DB, Schulz T, O'Brien KB, Verhaak RG, Delwel R, Haase D, Trumper L, Krauter J, Kohwi-Shigematsu T, Griesinger F, Tenen DG,. 2007. A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia. J Clin Invest 117: 2611-2620. (Pubitemid 47494362)
25. Unneberg P, Claverie JM,. 2007. Tentative mapping of transcription- induced interchromosomal interaction using chimeric EST and mRNA data. PLoS One 2: e254.
26. Xu M, Cook PR,. 2008. Similar active genes cluster in specialized transcription factories. J Cell Biol 181: 615-623. (Pubitemid 351717509)
27. Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R,. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38: 1341-1347. (Pubitemid 44646299)