Epigenetics of long-range chromatin interactions

Pediatric Research

Volumn 61, Issue 5 PART 2 SUPPL., 2007, Pages

  Ling, Jian Qun ^a   Hoffman, Andrew R ^a,b  

^a STANFORD UNIVERSITY   (United States)

^b VA PALO ALTO HEALTH CARE SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SPACER DNA;

ARTICLE; CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; CHROMOSOME 4Q; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA PROBE; DNA STRUCTURE; EPIGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE CONTROL; GENE INTERACTION; GENE LOCUS; GENE SILENCING; GENETIC RECOMBINATION; GENOME IMPRINTING; HUMAN; NONHUMAN; PRADER WILLI SYNDROME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; RADIATION CARCINOGENESIS; RECEPTOR GENE; STRUCTURE ANALYSIS; TH2 CELL; THYROID CANCER; TRANSCRIPTION REGULATION; X CHROMOSOME INACTIVATION;

ANIMALS; CELL NUCLEUS; CHROMATIN; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; HUMANS; LOCUS CONTROL REGION; NUCLEIC ACID CONFORMATION;

EID: 34247473070     PISSN: 00313998     EISSN: None     Source Type: Journal    
DOI: 10.1203/pdr.0b013e31804575db     Document Type: Article

References (59)

1. Feinberg AP, Ohlsson R, Henikoff S 2006 The epigenetic progenitor origin of human cancer. Nat Rev Genet 7:21-33
2. Turner BM 2002 Cellular memory and the histone code. Cell 111:285-291
3. Hake SB, Allis CD 2006 Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis." Proc Natl Acad Sci U S A 103:6428-6435
4. Li T, Vu TH, Ulaner GA, Yang Y, Hu JF, Hoffman AR 2004 Activating and silencing histone modifications form independent allelic switch regions in the imprinted Gnas gene. Hum Mol Genet 13:741-750
5. Fraga MF, Esteller M 2005 Towards the human cancer epigenome: a first draft of histone modifications. Cell Cycle 4:1377-1381
6. Laird PW 2005 Cancer epigenetics. Hum Mol Genet 14:R65-R76
7. Akhtar A, Cavalli G 2005 The epigenome network of excellence. PLoS Biol 3:e177
8. Parada LA, McQueen PG, Misteli T 2004 Tissue-specific spatial organization of genomes. Genome Biol 5:R44
9. Cremer T, Cremer C 2001 Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2:292-301
10. Cremer T, Creme C 2006 Rise, fall and resurrection of chromosome territories: a historical perspective. Part I. The rise of chromosome territories. Eur J Histochem 50:161-176
11. Cremer T, Kreth G, Koester H, Fink RH, Heintzmann R, Cremer M, Solovei I, Zink D, Cremer C 2000 Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture. Crit Rev Eukaryot Gene Expr 10:179-212
12. Branco MR, Pombo A, 2006 Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 4:e138
13. 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 U S A 103:10684-10689
14. Ling JQ, Li T, Hu JF, Vu TH, Chen HL, Qiu XW, Cherry AM, Hoffman AR 2006 CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312:269-272
15. 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
16. Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T 2005 Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet 37:31-40
17. Bagga R, Michalowski S, Sabnis R, Griffith JD, Emerson BM 2000 HMG I/Y regulates long-range enhancer-dependent transcription on DNA and chromatin by changes in DNA topology. Nucleic Acids Res 28:2541-2550
18. Yusufzai TM, Tagami H, Nakatani Y, Felsenfeld G 2004 CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol Cell 13:291-298
19. Cremer T, Cremer M, Dietzel S, Muller S, Solovei I, Fakan S 2006 Chromosome territories - a functional nuclear landscape. Curr Opin Cell Biol 18:307-316
20. Zink D, Fischer AH, Nickerson JA 2004 Nuclear structure in cancer cells. Nat Rev Cancer 4:677-687
21. 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
22. Nikiforova MN, Stringer JR, Blough R, Medvedovic M, Fagin JA, Nikiforov YE 2000 Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells. Science 290:138-141
23. Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T 2003 Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet 34:287-291
24. Parada LA, Sotiriou S, Misteli T 2004 Spatial genome organization. Exp Cell Res 296:64-70
25. Lopes S, Lewis A, Hajkova P, Dean W, Oswald J, Forne T, Murrell A, Constancia M, Bartolomei M, Walter J, Reik W 2003 Epigenetic modifications in an imprinting cluster are controlled by a hierarchy of DMRs suggesting long-range chromatin interactions. Hum Mol Genet 12:295-305
26. Sasaki H, Ishihara K, Kato R 2000 Mechanisms of Igf2/H19 imprinting: DNA methylation, chromatin and long-distance gene regulation. J Biochem (Tokyo) 127:711-715
27. Weber M, Hagege H, Murrell A, Brunel C, Reik W, Cathala G, Forne T 2003 Genomic imprinting controls matrix attachment regions in the Igf2 gene. Mol Cell Biol 23:8953-8959
28. Dekker J 2006 The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods 3:17-21
29. Dekker J, Rippe K, Dekker M, Kleckner N 2002 Capturing chromosome conformation. Science 295:1306-1311
30. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P 2002 Long-range chromatin regulatory interactions in vivo. Nat Genet 32:623-626
31. 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 10:1453-1465
32. Spilianakis CG, Flavell RA 2004 Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 5:1017-1027
33. 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
34. Eivazova ER, Aune TM 2004 Dynamic alterations in the conformation of the Ifng gene region during T helper cell differentiation. Proc Natl Acad Sci U S A 101:251-256
35. Liu Z, Garrard WT 2005 Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3′ boundary sequence spanning 46 kilobases. Mol Cell Biol 25:3220-3231
36. Fuxa M, Skok J, Souabni A, Salvagiotto G, Roldan E, Busslinger M 2004 Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene. Genes Dev 18:411-422
37. Kosak ST, Skok JA, Medina KL, Riblet R, Le Beau MM, Fisher AG, Singh H 2002 Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296:158-162
38. Sayegh C, Jhunjhunwala S, Riblet R, Murre C 2005 Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells. Genes Dev 19:322-327
39. Petrov A, Pirozhkova I, Carnac G, Laoudj D, Lipinski M, Vassetzky YS 2006 Chromatin loop domain organization within the 4q35 locus in facioscapulohumeral dystrophy patients versus normal human myoblasts. Proc Natl Acad Sci U S A 103:6982-6987
40. Fraser P 2006 Transcriptional control thrown for a loop. Curr Opin Genet Dev 16:490-495
41. LaSalle JM, Lalande M 1996 Homologous association of oppositely imprinted chromosomal domains. Science 272:725-728
42. Bacher CP, Guggiari M, Brors B, Augui S, Clerc P, Avner P, Eils R, Heard E 2006 Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol 8:293-299
43. Xu N, Tsai CL, Lee JT 2006 Transient homologous chromosome pairing marks the onset of X inactivation. Science 311:1149-1152
44. Kioussis D 2005 Gene regulation: kissing chromosomes. Nature 435:579-580
45. Morey C, Bickmore W 2006 Sealed with a X. Nat Cell Biol 8:207-209
46. Savage JR 1996 Insight into sites. Mutat Res 366:81-95
47. Spilianakis CG, Flavell RA 2006 Molecular biology. Managing associations between different chromosomes. Science 312:207-220
48. Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA 2005 Interchromosomal associations between alternatively expressed loci. Nature 435:637-645
49. Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, Wood WG, Higgs DR, Iborra FJ, Buckle VJ 2006 Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172:177-187
50. Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R 2006 Interchromosomal interactions and olfactory receptor choice. Cell 126:403-413
51. Bell AC, Felsenfeld G 2000 Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405:482-485
52. Kanduri C, Pant V, Loukinov D, Pugacheva E, Qi CF, Wolffe A, Ohlsson R, Lobanenkov VV 2000 Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr Biol 10:853-856
53. Szabo P, Tang SH, Rentsendorj A, Pfeifer GP, Mann JR 2000 Maternal-specific footprints at putative CTCF sites in the H19 imprinting control region give evidence for insulator function. Curr Biol 10:607-610
54. Szabo PE, Tang SH, Silva FJ, Tsark WM, Mann JR 2004 Role of CTCF binding sites in the Igf2/H19 imprinting control region. Mol Cell Biol 24:4791-4800
55. 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
56. Wurtele 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 14:477-495
57. 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
58. Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lezcano M, Singh Sandhu K, 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
59. Savarese F, Grosschedl R 2006 Blurring cis and trans in gene regulation. Cell 126:248-250