Window into the complexities of chromosome interactomes

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 75, Issue , 2010, Pages 493-500

  Gondor A ^a   Fernandez Woodbridge, A ^a,b   Shi, C ^a   Aurell, E ^b   Imreh, M ^a   Ohlsson, R ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; H19 PROTEIN; PROTEIN; TRANS ACTING FACTOR; TRANSCRIPTION FACTOR CTCF; UNCLASSIFIED DRUG; RNA H19;

ARTICLE; BINDING SITE; CHROMOSOME; CHROMOSOME 7; CHROMOSOME INTERACTOME; DNA METHYLATION; DROSOPHILA; EMBRYONIC STEM CELL; EPIGENETICS; GENE DELETION; GENE EXPRESSION; GENE FUNCTION; GENE INSERTION; GENE MUTATION; GENE TARGETING; GENE TRANSFER; GENOME IMPRINTING; HUMAN; IMPRINTING CONTROL REGION; NONHUMAN; PRIORITY JOURNAL; PROTEIN METHYLATION; REGULATOR GENE; CIS TRANS ISOMERISM; GENE CONTROL; GENETIC TRAIT; MOLECULAR INTERACTION;

ANIMALS; CHROMATIN; CHROMOSOMES; EMBRYOID BODIES; EPIGENESIS, GENETIC; GENOMIC IMPRINTING; HUMANS; MODELS, BIOLOGICAL; REPRESSOR PROTEINS; RNA, UNTRANSLATED;

EID: 80052406383     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2010.75.049     Document Type: Article

References (30)

1. Apostolou E, Thanos D. 2008. Virus infection induces NF-κB-dependent interchromosomal associations mediating monoallelic IFN-β gene expression. Cell 134: 85-96.
2. Barabasi AL, Albert R. 1999. Emergence of scaling in random networks. Science 286: 509-512.
3. Bergstrom R, Whitehead J, Kurukuti S, Ohlsson R. 2007. CTCF regulates asynchronous replication of the imprinted H19/Igf2 domain. Cell Cycle 6: 450-454.
4. Cai S, Lee CC, Kohwi-Shigematsu T. 2006. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet 38: 1278-1288.
5. Constancia M, Dean W, Lopes S, Moore T, Kelsey G, Reik W. 2000. Deletion of a silencer element in Igf2 results in loss of imprinting independent of H19. Nat Genet 26: 203-206.
6. Dekker J. 2006. The three 'C's of chromosome conformation capture: Controls, controls, controls. Nat Methods 3: 17-21.
7. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, et al. 2006. Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res 16: 1299-1309.
8. Duncan IW. 2002. Transvection effects in Drosophila. Annu Rev Genet 36: 521-556.
9. Göndör A, Ohlsson R. 2009a. Chromosome crosstalk in three dimensions. Nature 461: 212-217.
10. Göndör A, Ohlsson R. 2009b. Replication timing and epigenetic reprogramming of gene expression: A two-way relationship? Nat Rev Genet 10: 269-276.
11. Hou C, Corces VG. 2010. Insulators and imprinting from flies to mammals. BMC Biol 8: 104. doi: 10.1186/1741-7007-8-104.
12. Kaiser TE, Intine RV, Dundr M. 2008. De novo formation of a subnuclear body. Science 322: 1713-1717.
13. Kanduri M, Kanduri C, Mariano P, Vostrov AA, Quitschke W, Lobanenkov V, Ohlsson R. 2002. Multiple nucleosome positioning sites regulate the CTCF-mediated insulator function of the H19 imprinting control region. Mol Cell Biol 22: 3339-3344.
14. Kaneda A, Wang CJ, Cheong R, Timp W, Onyango P, Wen B, Iacobuzio-Donahue CA, Ohlsson R, Andraos R, Pearson MA, et al. 2007. Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk. Proc Natl Acad Sci 104: 20926-20931.
15. Kurukuti S, Tiwari VK, Tavoosidana G, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W, Ohlsson R. 2006. 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 103: 10684-10689.
16. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
17. Maslov S, Sneppen K. 2002. Specificity and stability in topology of protein networks. Science 296: 910-913.
18. Murrell A, Heeson S, Reik W. 2004. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet 36: 889- 893.
19. Nativio R, Wendt KS, Ito Y, Huddleston JE, Uribe-Lewis S, Woodfine K, Krueger C, Reik W, Peters JM, Murrell A. 2009. Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus. PLoS Genet 5: e1000739. doi: 10.1371/journal.pgen.1000739.
20. Ohlsson R, Lobanenkov V, Klenova E. 2010. Does CTCF mediate between nuclear organization and gene expression? Bioessays 32: 37-50.
21. Pant V, Mariano P, Kanduri C, Mattsson A, Lobanenkov V, Heuchel R, Ohlsson R. 2003. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. Genes Dev 17: 586-590.
22. Sakatani T, Kaneda A, Iacobuzio-Donahue CA, Carter MG, de Boom Witzel S, Okano H, Ko MS, Ohlsson R, Longo DL, Feinberg AP. 2005. Loss of imprinting of Igf2 alters intestinal maturation and tumorigenesis in mice. Science 307: 1976-1978.
23. Sandhu KS, Shi C, Sjolinder M, Zhao Z, Göndör 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.
24. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, et al. 2010. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42: 53-61.
25. 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.
26. Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA. 2005. Interchromosomal associations between alternatively expressed loci. Nature 435: 637-645.
27. Sumida N, Ohlsson R. 2010. Chromosomal networks as mediators of epigenetic states: The maternal genome connection. Epigenetics 5: 297-300.
28. Wallace JA, Felsenfeld G. 2007. We gather together: Insulators and genome organization. Curr Opin Genet Dev 17: 400-407.
29. Webber AL, Ingram RS, Levorse JM, Tilghman SM. 1998. Location of enhancers is essential for the imprinting of H19 and Igf2 genes. Nature 391: 711-715.
30. Zhao Z, Tavoosidana G, Sjolinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, et al. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38: 1341-1347.