Long range chromatin interactions involved in gene regulation

Biochimica et Biophysica Acta - Molecular Cell Research

Volumn 1783, Issue 11, 2008, Pages 2161-2166

  Bartkuhn, Marek ^a   Renkawitz, Rainer ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

Chromatin; CTCF; Enhancer; Imprinting; Three dimensional interaction

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CTCF; UNCLASSIFIED DRUG;

CHROMOSOME PAIRING; ENHANCER REGION; EPIGENETICS; GENE CONTROL; GENE INTERACTION; GENOME IMPRINTING; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY SEQUENCE; REVIEW;

ANIMALS; CHROMATIN; CHROMOSOMES; DNA-BINDING PROTEINS; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; HUMANS; REGULATORY SEQUENCES, NUCLEIC ACID; REPRESSOR PROTEINS; TRANSCRIPTION FACTORS;

EID: 53249121024     PISSN: 01674889     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamcr.2008.07.011     Document Type: Review

References (80)

1. Mueller-Storm H.P., Sogo J.M., and Schaffner W. An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge. Cell 58 (1989) 767-777
2. Dekker J., Rippe K., Dekker M., and Kleckner N. Capturing chromosome conformation. Science 295 (2002) 1306-1311
3. Gothard L.Q., Hibbard J.C., and Seyfred M.A. Estrogen-mediated induction of rat prolactin gene transcription requires the formation of a chromatin loop between the distal enhancer and proximal promoter regions. Mol. Endocrinol. 10 (1996) 185-195
4. Hatzis P., and Talianidis I. Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol. Cell 10 (2002) 1467-1477
5. Liu Z., and Garrard W.T. Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3′ boundary sequence spanning 46 kilobases. Mol. Cell Biol. 25 (2005) 3220-3231
6. Jing H., Vakoc C.R., Ying L., Mandat S., Wang H., Zheng X., and Blobel G.A. Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. Mol. Cell 29 (2008) 232-242
7. Lewis E.B. The theory and application of a new method of detecting chromosomal rearrangements in Drosophila melanogaster. Am. Nat. 88 (1954) 225-239
8. Geyer P.K., Green M.M., and Corces V.G. Tissue-specific transcriptional enhancers may act in trans on the gene located in the homologous chromosome: the molecular basis of transvection in Drosophila. Embo. J. 9 (1990) 2247-2256
9. Bantignies F., Grimaud C., Lavrov S., Gabut M., and Cavalli G. Inheritance of polycomb-dependent chromosomal interactions in Drosophila. Genes Dev. 17 (2003) 2406-2420
10. Muller M., Hagstrom K., Gyurkovics H., Pirrotta V., and Schedl P. The mcp element from the Drosophila melanogaster bithorax complex mediates long-distance regulatory interactions. Genetics 153 (1999) 1333-1356
11. Grimaud C., Bantignies F., Pal-Bhadra M., Ghana P., Bhadra U., and Cavalli G. RNAi components are required for nuclear clustering of Polycomb group response elements. Cell 124 (2006) 957-971
12. Lomvardas S., Barnea G., Pisapia D.J., Mendelsohn M., Kirkland J., and Axel R. Interchromosomal interactions and olfactory receptor choice. Cell 126 (2006) 403-413
13. Serizawa S., Miyamichi K., Nakatani H., Suzuki M., Saito M., Yoshihara Y., and Sakano H. Negative feedback regulation ensures the one receptor-one olfactory neuron rule in mouse. Science 302 (2003) 2088-2094
14. Udvardy A., Maine E., and Schedl P. The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains. J. Mol. Biol. 185 (1985) 341-358
15. Gaszner M., Vazquez J., and Schedl P. The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer-promoter interaction. Genes Dev. 13 (1999) 2098-2107
16. Zhao K., Hart C.M., and Laemmli U.K. Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell 81 (1995) 879-889
17. Blanton J., Gaszner M., and Schedl P. Protein:protein interactions and the pairing of boundary elements in vivo. Genes Dev. 17 (2003) 664-675
18. Spana C., Harrison D.A., and Corces V.G. The Drosophila melanogaster suppressor of Hairy-wing protein binds to specific sequences of the gypsy retrotransposon. Genes Dev. 2 (1988) 1414-1423
19. Lei E.P., and Corces V.G. RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat. Genet. 38 (2006) 936-941
20. Gerasimova T.I., Gdula D.A., Gerasimov D.V., Simonova O., and Corces V.G. A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation. Cell 82 (1995) 587-597
21. Pai C.Y., Lei E.P., Ghosh D., and Corces V.G. The centrosomal protein CP190 is a component of the gypsy chromatin insulator. Mol. Cell 16 (2004) 737-748
22. Capelson M., and Corces V.G. The ubiquitin ligase dTopors directs the nuclear organization of a chromatin insulator. Mol. Cell 20 (2005) 105-116
23. Adryan B., Woerfel G., Birch-Machin I., Gao S., Quick M., Meadows L., Russell S., and White R. Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila. Genome. Biol. 8 (2007) R167
24. Ramos E., Ghosh D., Baxter E., and Corces V.G. Genomic organization of gypsy chromatin insulators in Drosophila melanogaster. Genetics 172 (2006) 2337-2349
25. Parnell T.J., Kuhn E.J., Gilmore B.L., Helou C., Wold M.S., and Geyer P.K. Identification of genomic sites that bind the Drosophila suppressor of Hairy-wing insulator protein. Mol. Cell Biol. 26 (2006) 5983-5993
26. Lewis E.B. A gene complex controlling segmentation in Drosophila. Nature 276 (1978) 565-570
27. Sanchez-Herrero E., Vernos I., Marco R., and Morata G. Genetic organization of Drosophila bithorax complex. Nature 313 (1985) 108-113
28. Maeda R.K., and Karch F. The ABC of the BX-C: the bithorax complex explained. Development 133 (2006) 1413-1422
29. Kyrchanova O., Toshchakov S., Parshikov A., and Georgiev P. Study of the functional interaction between Mcp insulators from the Drosophila bithorax complex: effects of insulator pairing on enhancer-promoter communication. Mol. Cell Biol. 27 (2007) 3035-3043
30. Vazquez J., Muller M., Pirrotta V., and Sedat J.W. The Mcp element mediates stable long-range chromosome-chromosome interactions in Drosophila. Mol. Biol. Cell 17 (2006) 2158-2165
31. Cleard F., Moshkin Y., Karch F., and Maeda R.K. Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification. Nat. Genet. 38 (2006) 931-935
32. Lanzuolo C., Roure V., Dekker J., Bantignies F., and Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat. Cell Biol. 9 (2007) 1167-1174
33. Schweinsberg S., Hagstrom K., Gohl D., Schedl P., Kumar R.P., Mishra R., and Karch F. The enhancer-blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA-factor-binding sites. Genetics 168 (2004) 1371-1384
34. Holohan E.E., Kwong C., Adryan B., Bartkuhn M., Herold M., Renkawitz R., Russell S., and White R. CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex. PloS Genetics 3 (2007) e112
35. Mohan M., Bartkuhn M., Herold M., Philippen A., Heinl N., Bardenhagen I., Leers J., White R.A., Renkawitz-Pohl R., Saumweber H., and Renkawitz R. The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning. Embo. J. 26 (2007) 4203-4214
36. Moon H., Filippova G., Loukinov D., Pugacheva E., Chen Q., Smith S.T., Munhall A., Grewe B., Bartkuhn M., Arnold R., Burke L.J., Renkawitz-Pohl R., Ohlsson R., Zhou J., Renkawitz R., and Lobanenkov V. CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator. EMBO. Rep. 6 (2005) 165-170
37. Robertson K.D. DNA methylation and human disease. Nat. Rev. Genet. 6 (2005) 597-610
38. Wallace J.A., and Felsenfeld G. We gather together: insulators and genome organization. Curr. Opin. Genet. Dev. 17 (2007) 400-407
39. Burke L.J., Zhang R., Bartkuhn M., Tiwari V.K., Tavoosidana G., Kurukuti S., Weth C., Leers J., Galjart N., Ohlsson R., and Renkawitz R. CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin. Embo. J. 24 (2005) 3291-3300
40. Kurukuti S., Tiwari V.K., Tavoosidana G., Pugacheva E., Murrell A., Zhao Z., Lobanenkov V., Reik W., and Ohlsson R. 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 (2006) 10684-10689
41. Murrell A., Heeson S., and Reik W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36 (2004) 889-893
42. Qiu X., Vu T.H., Lu Q., Ling J.Q., Li T., Hou A., Wang S.K., Chen H.L., Hu J.F., and Hoffman A.R. A complex DNA looping configuration associated with the silencing of the maternal Igf2 allele. Mol. Endocrinol. (2008)
43. Yoon Y.S., Jeong S., Rong Q., Park K.Y., Chung J.H., and Pfeifer K. Analysis of the H19ICR insulator. Mol. Cell Biol. 27 (2007) 3499-3510
44. Han L., Lee D.H., and Szabo P.E. CTCF is the master organizer of domain-wide allele-specific chromatin at the H19/Igf2 imprinted region. Mol. Cell Biol. 28 (2008) 1124-1135
45. Mahajan M.C., Karmakar S., and Weissman S.M. Control of beta globin genes. J. Cell Biochem. 102 (2007) 801-810
46. Tolhuis B., Palstra R.J., Splinter E., Grosveld F., and de Laat W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell 10 (2002) 1453-1465
47. Splinter E., Heath H., Kooren J., Palstra R.J., Klous P., Grosveld F., Galjart N., and de Laat W. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev. 20 (2006) 2349-2354
48. Majumder P., Gomez J.A., Chadwick B.P., and Boss J.M. The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions. J. Exp. Med. 205 (2008) 785-798
49. Osborne C.S., Chakalova L., Brown K.E., Carter D., Horton A., Debrand E., Goyenechea B., Mitchell J.A., Lopes S., Reik W., and Fraser P. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36 (2004) 1065-1071
50. Spilianakis C.G., Lalioti M.D., Town T., Lee G.R., and Flavell R.A. Interchromosomal associations between alternatively expressed loci. Nature 435 (2005) 637-645
51. Gondor A., Rougier C., and Ohlsson R. High-resolution circular chromosome conformation capture assay. Nat. Protoc. 3 (2008) 303-313
52. Wurtele H., and Chartrand P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended chromosome conformation capture methodology. Chromosome Res. 14 (2006) 477-495
53. Simonis M., Klous P., Splinter E., Moshkin Y., Willemsen R., de Wit E., van Steensel B., and de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38 (2006) 1348-1354
54. Nunez E., Kwon Y.S., Hutt K.R., Hu Q., Cardamone M.D., Ohgi K.A., Garcia-Bassets I., Rose D.W., Glass C.K., Rosenfeld M.G., and Fu X.D. Nuclear receptor-enhanced transcription requires motor- and LSD1-dependent gene networking in interchromatin granules. Cell 132 (2008) 996-1010
55. Ling J.Q., Li T., Hu J.F., Vu T.H., Chen H.L., Qiu X.W., Cherry A.M., and Hoffman A.R. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312 (2006) 269-272
56. Zhao Z., Tavoosidana G., Sjolinder M., Gondor A., Mariano P., Wang S., Kanduri C., Lezcano M., Sandhu K.S., Singh U., Pant V., Tiwari V., Kurukuti S., and Ohlsson R. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38 (2006) 1341-1347
57. Baniahmad A., Steiner C., Kohne A.C., and Renkawitz R. Modular structure of a chicken lysozyme silencer: involvement of an unusual thyroid hormone receptor binding site. Cell 61 (1990) 505-514
58. Lobanenkov V.V., Nicolas R.H., Adler V.V., Paterson H., Klenova E.M., Polotskaja A.V., and Goodwin G.H. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5′-flanking sequence of the chicken c-myc gene. Oncogene 5 (1990) 1743-1753
59. Ohlsson R., Renkawitz R., and Lobanenkov V. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet. 17 (2001) 520-527
60. Filippova G.N., Qi C.F., Ulmer J.E., Moore J.M., Ward M.D., Hu Y.J., Loukinov D.I., Pugacheva E.M., Klenova E.M., Grundy P.E., Feinberg A.P., Cleton-Jansen A.M., Moerland E.W., Cornelisse C.J., Suzuki H., Komiya A., Lindblom A., Dorion-Bonnet F., Neiman P.E., Morse III H.C., Collins S.J., and Lobanenkov V.V. Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter its DNA-binding specificity. Cancer Res. 62 (2002) 48-52
61. Fedoriw A.M., Stein P., Svoboda P., Schultz R.M., and Bartolomei M.S. Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting. Science 303 (2004) 238-240
62. Chao W., Huynh K.D., Spencer R.J., Davidow L.S., and Lee J.T. CTCF, a candidate trans-acting factor for X-inactivation choice. Science 295 (2002) 345-347
63. Xu N., Donohoe M.E., Silva S.S., and Lee J.T. Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat. Genet. 39 (2007) 1390-1396
64. Bacher C.P., Guggiari M., Brors B., Augui S., Clerc P., Avner P., Eils R., and Heard E. Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat. Cell Biol. 8 (2006) 293-299
65. Pant V., Kurukuti S., Pugacheva E., Shamsuddin S., Mariano P., Renkawitz R., Klenova E., Lobanenkov V., and Ohlsson R. Mutation of a single CTCF target site within the H19 imprinting control region leads to loss of Igf2 imprinting and complex patterns of de novo methylation upon maternal inheritance. Mol. Cell Biol. 24 (2004) 3497-3504
66. Yusufzai T.M., Tagami H., Nakatani Y., and Felsenfeld G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol. Cell 13 (2004) 291-298
67. Parelho V., Hadjur S., Spivakov M., Leleu M., Sauer S., Gregson H.C., Jarmuz A., Canzonetta C., Webster Z., Nesterova T., Cobb B.S., Yokomori K., Dillon N., Aragon L., Fisher A.G., and Merkenschlager M. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132 (2008) 422-433
68. Stedman W., Kang H., Lin S., Kissil J.L., Bartolomei M.S., and Lieberman P.M. Cohesins localize with CTCF at the KSHV latency control region and at cellular c-myc and H19/Igf2 insulators. Embo. J. 27 (2008) 654-666
69. Wendt K.S., Yoshida K., Itoh T., Bando M., Koch B., Schirghuber E., Tsutsumi S., Nagae G., Ishihara K., Mishiro T., Yahata K., Imamoto F., Aburatani H., Nakao M., Imamoto N., Maeshima K., Shirahige K., and Peters J.M. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451 (2008) 796-801
70. Nasmyth K., and Haering C.H. The structure and function of SMC and kleisin complexes. Annu. Rev. Biochem. 74 (2005) 595-648
71. Losada A., Hirano M., and Hirano T. Identification of Xenopus SMC protein complexes required for sister chromatid cohesion. Genes Dev. 12 (1998) 1986-1997
72. Klose R.J., and Bird A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31 (2006) 89-97
73. Renda M., Baglivo I., Burgess-Beusse B., Esposito S., Fattorusso R., Felsenfeld G., and Pedone P.V. Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci. J. Biol. Chem. 282 (2007) 33336-33345
74. Xie X., Mikkelsen T.S., Gnirke A., Lindblad-Toh K., Kellis M., and Lander E.S. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 7145-7150
75. Kim T.H., Abdullaev Z.K., Smith A.D., Ching K.A., Loukinov D.I., Green R.D., Zhang M.Q., Lobanenkov V.V., and Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128 (2007) 1231-1245
76. Zaidi S.K., Young D.W., Pockwinse S.M., Javed A., Lian J.B., Stein J.L., van Wijnen A.J., and Stein G.S. Mitotic partitioning and selective reorganization of tissue-specific transcription factors in progeny cells. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 14852-14857
77. Martinez-Balbas M.A., Dey A., Rabindran S.K., Ozato K., and Wu C. Displacement of sequence-specific transcription factors from mitotic chromatin. Cell 83 (1995) 29-38
78. Gottesfeld J.M., and Forbes D.J. Mitotic repression of the transcriptional machinery. Trends Biochem. Sci. 22 (1997) 197-202
79. Dovat S., Ronni T., Russell D., Ferrini R., Cobb B.S., and Smale S.T. A common mechanism for mitotic inactivation of C2H2 zinc finger DNA-binding domains. Genes Dev. 16 (2002) 2985-2990
80. Kruhlak M.J., Hendzel M.J., Fischle W., Bertos N.R., Hameed S., Yang X.J., Verdin E., and Bazett-Jones D.P. Regulation of global acetylation in mitosis through loss of histone acetyltransferases and deacetylases from chromatin. J. Biol. Chem. 276 (2001) 38307-38319