3C-based methods to detect long-range chromatin interactions

Frontiers of Biology in China

Volumn 6, Issue 1, 2011, Pages 76-81

  Wei, Gang ^a   Zhao, Keji ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

3C; chromatin interactions; gene regulation; next generation sequencing

Indexed keywords

EID: 79251607477     PISSN: 16733509     EISSN: 16733622     Source Type: Journal    
DOI: 10.1007/s11515-011-0980-6     Document Type: Review

References (33)

1. Barski A, Cuddapah S, Cui K R, Roh T Y, Schones D E, Wang Z B, Wei G, Chepelev I, Zhao K (2007). High-resolution profiling of histone methylations in the human genome. Cell, 129(4): 823-837.
2. Boyle A P, Davis S, Shulha H P, Meltzer P, Margulies E H, Weng Z, Furey T S, Crawford G E (2008). High-resolution mapping and characterization of open chromatin across the genome. Cell, 132(2): 311-322.
3. Cai S T, Lee C C, Kohwi-Shigematsu T (2006). SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet, 38(11): 1278-1288.
4. Carroll J S, Liu X S, Brodsky A S, Li W, Meyer C A, Szary A J, Eeckhoute J, Shao W L, Hestermann E V, Geistlinger T R, Fox E A, Silver P A, Brown M (2005). Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell, 122(1): 33-43.
5. Carter D, Chakalova L, Osborne C S, Dai Y F, Fraser P (2002). Longrange chromatin regulatory interactions in vivo. Nat Genet, 32(4): 623-626.
6. Dekker J, Rippe K, Dekker M, Kleckner N (2002). Capturing chromosome conformation. Science, 295(5558): 1306-1311.
7. Dostie J, Dekker J (2006). Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc, 2, 988-1002.
8. Dostie J, Richmond T A, Arnaout R A, Selzer R R, Lee WL, Honan T A, Rubio E D, Krumm A, Lamb J, Nusbaum C, Green R D, Dekker J (2006). Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res, 16(10): 1299-1309.
9. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim Y J, Lee C, Shendure J, Fields S, Blau C A, Noble W S (2010). A threedimensional model of the yeast genome. Nature, 465(7296): 363-367.
10. ENCODE project consortium (2004). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306(5696): 636-640.
11. Fullwood M J, Liu M H, Pan Y F, Liu J, Xu H, Mohamed Y B, Orlov Y L, Velkov S, Ho A, Mei P H, Chew E G, Huang P Y, Welboren W J, Han Y, Ooi H S, Ariyaratne P N, Vega V B, Luo Y, Tan P Y, Choy P Y, Wansa K D, Zhao B, Lim K S, Leow S C, Yow J S, Joseph R, Li H, Desai K V, Thomsen J S, Lee Y K, Karuturi R K, Herve T, Bourque G, Stunnenberg H G, Ruan X, Cacheux-Rataboul V, Sung W K, Liu E T, Wei C L, Cheung E, Ruan Y (2009). An oestrogen-receptoralpha-bound human chromatin interactome. Nature, 462(7269): 58-64.
12. Göndör A, Ohlsson R (2009). Chromosome crosstalk in three dimensions. Nature, 461(7261): 212-217.
13. Horike S, Cai S T, Miyano M, Cheng J F, Kohwi-Shigematsu T (2005). Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet, 37(1): 31-40.
14. Johnson D S, Mortazavi A, Myers R M, Wold B (2007). Genome-wide mapping of in vivo protein-DNA interactions. Science, 316(5830): 1497-1502.
15. Kim S I, Bresnick E H, Bultman S J (2009). BRG1 directly regulates nucleosome structure and chromatin looping of the alpha globin locus to activate transcription. Nucleic Acids Res, 37(18): 6019-6027.
16. Lajoie B R, van Berkum N L, Sanyal A, Dekker J (2009). My5C: web tools for chromosome conformation capture studies. Nat Methods, 6 (10): 690-691.
17. Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T (2007). Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet, 8(2): 104-115.
18. Lieberman-Aiden E, van Berkum N L, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B R, Sabo P J, Dorschner M O, Sandstrom R, Bernstein B, Bender M A, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny L A, Lander E S, Dekker J (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326(5950): 289-293.
19. Misteli T (2007). Beyond the sequence: cellular organization of genome function. Cell, 128(4): 787-800.
20. 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(8): 889-893.
21. Palstra R J, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, de Laat W (2003). The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet, 35(2): 190-194.
22. Schones D E, Cui K, Cuddapah S, Roh T Y, Barski A, Wang Z, Wei G, Zhao K (2008). Dynamic regulation of nucleosome positioning in the human genome. Cell, 132(5): 887-898.
23. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, deWit 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(11): 1348-1354.
24. Spilianakis C G, Flavell R A (2004). Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol, 5 (10): 1017-1027.
25. Spilianakis C G, Lalioti M D, Town T, Lee G R, Flavell R A (2005). Interchromosomal associations between alternatively expressed loci. Nature, 435(7042): 637-645.
26. Splinter E, Heath H, Kooren J, Palstra R J, Klous P, Grosveld F, Galjart N, de Laat W (2006). CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev, 20(17): 2349-2354.
27. Tiwari V K, Cope L, McGarvey K M, Ohm J E, Baylin S B (2008). A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res, 18(7): 1171-1179.
28. Tolhuis B, Palstra R J, Splinter E, Grosveld F, de Laat W (2002). Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell, 10(6): 1453-1465.
29. Vakoc C R, Letting D L, Gheldof N, Sawado T, Bender M A, Groudine M, Weiss MJ, Dekker J, Blobel G A (2005). Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell, 17(3): 453-462.
30. Wang Z, Schones D E, Zhao K (2009). Characterization of human epigenomes. Curr Opin Genet Dev, 19(2): 127-134.
31. Würtele H, Chartrand P (2006). Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res, 14(5): 477-495.
32. Xu N, Tsai C L, Lee J T (2006). Transient homologous chromosome pairing marks the onset of X inactivation. Science, 311(5764): 1149-1152.
33. Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu K S, 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(11): 1341-1347.