Analysis of chromatin boundary activity in Drosophila cells

BMC Molecular Biology

Volumn 9, Issue , 2008, Pages

  Li, Mo ^a   Belozerov, Vladimir E ^a   Cai, Haini N ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA;

ANIMAL CELL; ARTICLE; CHROMATIN; CONTROLLED STUDY; DROSOPHILA; ENHANCER REGION; GENE ACTIVITY; GENE DISRUPTION; GENE FUNCTION; INSECT CELL CULTURE; INSECT GENETICS; INSULATOR ELEMENT; NONHUMAN; QUANTITATIVE ANALYSIS; REGULATOR GENE; RNA INTERFERENCE; ANIMAL; CELL CULTURE; CHEMISTRY; GENETIC PROCEDURES; GENETICS; METABOLISM;

ANIMALS; CELLS, CULTURED; CHROMATIN; DROSOPHILA; ENHANCER ELEMENTS, GENETIC; GENETIC TECHNIQUES; INSULATOR ELEMENTS; RNA INTERFERENCE;

EID: 58249113950     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-9-109     Document Type: Article

References (71)

1. Celniker SE Drewell RA Chromatin looping mediates boundary element promoter interactions Bioessays 2007, 29(1):7-10. 17187351
2. Wallace JA Felsenfeld G We gather together: Insulators and genome organization Curr Opin Genet Dev 2007, 17(5):400-407. 2215060 17913488
3. Wei GH Liu de P Liang CC Chromatin domain boundaries: Insulators and beyond Cell Res 2005, 15(4):292-300. 15857584
4. Cai HN Function and mechanism of chromatin boundaries Gene Expression and Regulation Beijing: Higher Education Press Ma J 2006.
5. Sipos L Gyurkovics H Long-distance interactions between enhancers and promoters Febs J 2005, 272(13):3253-3259. 15978032
6. Capelson M Corces VG Boundary elements and nuclear organization Biol Cell 2004, 96(8):617-629. 15519696
7. Valenzuela L Kamakaka RT Chromatin insulators Annu Rev Genet 2006, 40:107-138. 16953792
8. Gaszner M Felsenfeld G Insulators: Exploiting transcriptional and epigenetic mechanisms Nat Rev Genet 2006, 7(9):703-713. 16909129
9. Kellum R Schedl P A position-effect assay for boundaries of higher order chromosomal domains Cell 1991, 64(5):941-950. 1848159
10. Kellum R Schedl P A group of scs elements function as domain boundaries in an enhancer- blocking assay Mol Cell Biol 1992, 12(5):2424-2431. 364415 1569958
11. Donze D Adams CR Rine J Kamakaka RT The boundaries of the silenced HMR domain in Saccharomyces cerevisiae Genes Dev 1999, 13(6):698-708. 316548 10090726
12. Donze D Kamakaka RT RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae Embo J 2001, 20(3):520-531. 133458 11157758
13. Bi X Broach JR Chromosomal boundaries in S. cerevisiae Curr Opin Genet Dev 2001, 11(2):199-204. 11250144
14. Ferrari S Simmen KC Dusserre Y Muller K Fourel G Gilson E Mermod N Chromatin domain boundaries delimited by a histone-binding protein in yeast J Biol Chem 2004, 279(53):55520-55530. 15471882
15. Hark AT Schoenherr CJ Katz DJ Ingram RS Levorse JM Tilghman SM CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/ Igf2 locus Nature 2000, 405(6785):486-489. 10839547
16. Bell AC Felsenfeld G Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene Nature 2000, 405(6785):482-485. 10839546
17. Geyer PK Corces VG Separate regulatory elements are responsible for the complex pattern of tissue-specific and developmental transcription of the yellow locus in Drosophila melanogaster Genes Dev 1987, 1(9):996-1004. 3123324
18. Cai H Levine M Modulation of enhancer-promoter interactions by insulators in the Drosophila embryo Nature 1995, 376(6540):533-536. 7637789
19. Scott KS Geyer PK Effects of the su(Hw) insulator protein on the expression of the divergently transcribed Drosophila yolk protein genes Embo J 1995, 14(24):6258-6267. 394750 8557045
20. Morcillo P Rosen C Dorsett D Genes regulating the remote wing margin enhancer in the Drosophila cut locus Genetics 1996, 144(3):1143-1154. 1207607 8913756
21. Yao S Osborne CS Bharadwaj RR Pasceri P Sukonnik T Pannell D Recillas-Targa F West AG Ellis J Retrovirus silencer blocking by the cHS4 insulator is CTCF independent Nucleic Acids Res 2003, 31(18):5317-5323. 203325 12954767
22. Bell AC West AG Felsenfeld G The protein CTCF is required for the enhancer blocking activity of vertebrate insulators Cell 1999, 98(3):387-396. 10458613
23. Chung JH Whiteley M Felsenfeld G A 5′ element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila Cell 1993, 74:505-514. 8348617
24. Recillas-Targa F Pikaart MJ Burgess-Beusse B Bell AC Litt MD West AG Gaszner M Felsenfeld G Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities Proc Natl Acad Sci USA 2002, 99(10):6883-6888. 124498 12011446
25. West AG Huang S Gaszner M Litt MD Felsenfeld G Recruitment of histone modifications by USF proteins at a vertebrate barrier element Mol Cell 2004, 16(3):453-463. 15525517
26. Recillas-Targa F Bell AC Felsenfeld G Positional enhancer-blocking activity of the chicken beta-globin insulator in transiently transfected cells Proc Natl Acad Sci USA 1999, 96(25):14354-14359. 24440 10588709
27. Zhou J Barolo S Szymanski P Levine M The Fab-7 element of the bithorax complex attenuates enhancer-promoter interactions in the Drosophila embryo Genes Dev 1996, 10(24):3195-3201. 8985187
28. Zhou J Ashe H Burks C Levine M Characterization of the transvection mediating region of the abdominal- B locus in Drosophila Development 1999, 126(14):3057-3065. 10375498
29. Hagstrom K Schedl P Remembrance of things past: Maintaining gene expression patterns with altered chromatin Curr Opin Genet Dev 1997, 7(6):814-821. 9468792
30. Barges S Mihaly J Galloni M Hagstrom K Muller M Shanower G Schedl P Gyurkovics H Karch F The Fab-8 boundary defines the distal limit of the bithorax complex iab-7 domain and insulates iab-7 from initiation elements and a PRE in the adjacent iab-8 domain Development 2000, 127(4):779-790. 10648236
31. Belozerov VE Majumder P Shen P Cai HN A novel boundary element may facilitate independent gene regulation in the Antennapedia Complex of Drosophila EMBO J 2003, 22:12. 162149 12805225
32. Majumder P Cai HN The functional analysis of insulator interactions in the Drosophila embryo Proc Natl Acad Sci USA 2003, 100(9):5223-5228. 154326 12700350
33. Cai HN Shen P Effects of cis arrangement of chromatin insulators on enhancer-blocking activity Science 2001, 291(5503):493-495. 11161205
34. Parkhurst SM Corces VG Interactions among the gypsy transposable element and the yellow and the suppressor of hairy-wing loci in Drosophila melanogaster Mol Cell Biol 1986, 6:47-53. 367482 3023836
35. Spana C Harrison DA Corces VG The Drosophila melanogaster suppressor of Hairy-wing protein binds to specific sequences of the gypsy retrotransposon Genes Dev 1988, 2(11):1414-1423. 2850261
36. Moon H Filippova G Loukinov D Pugacheva E Chen Q Smith ST Munhall A Grewe B Bartkuhn M Arnold R Burke LJ Renkawitz-Pohl R Ohlsson R Zhou J Renkawitz R Lobanenkov V CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator EMBO Rep 2005, 6(2):165-170. 1299244 15678159
37. Boutros M Kiger AA Armknecht S Kerr K Hild M Koch B Haas SA Consortium HF Paro R Perrimon N Genome-wide RNAi analysis of growth and viability in Drosophila cells Science 2004, 303(5659):832-835. 14764878
38. Small S Blair A Levine M Regulation of even-skipped stripe 2 in the Drosophila embryo Embo J 1992, 11(11):4047-4057. 556915 1327756
39. Ohtsuki S Levine M GAGA mediates the enhancer blocking activity of the eve promoter in the Drosophila embryo Genes Dev 1998, 12(21):3325-3330. 317233 9808619
40. Cai HN Levine M The gypsy insulator can function as a promoter-specific silencer in the Drosophila embryo EMBO J 1997, 16(7):1732-1741. 1169776 9130717
41. Cai HN Zhang Z Adams JR Shen P Genomic context modulates insulator activity through promoter competition Development 2001, 128(21):4339-4347. 11684668
42. Barolo S Castro B Posakony JW New Drosophila transgenic reporters: insulated P-element vectors expressing fast-maturing RFP Biotechniques 2004, 36(3):436-440. 442 15038159
43. Bunch TA Grinblat Y Goldstein LS Characterization and use of the Drosophila metallothionein promoter in cultured Drosophila melanogaster cells Nucleic Acids Res 1988, 16(3):1043-1061. 334736 3125519
44. Echalier G Ohanessian A In vitro culture of Drosophila melanogaster embryonic cells In Vitro 1970, 6(3):162-172. 5002052
45. Echalier G Ohanessian A [Isolation, in tissue culture, of Drosophila melangaster cell lines] C R Acad Sci Hebd Seances Acad Sci D 1969, 268(13):1771-1773. 4976834
46. Segal D Cherbas L Cherbas P Genetic transformation of Drosophila cells in culture by P element-mediated transposition Somat Cell Mol Genet 1996, 22(2):159-165. 8782495
47. Dorer DR Henikoff S Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila Cell 1994, 77(7):993-1002. 8020105
48. Henikoff S Dreesen TD Trans-inactivation of the Drosophila brown gene: evidence for transcriptional repression and somatic pairing dependence Proc Natl Acad Sci USA 1989, 86(17):6704-6708. 297914 2505257
49. Dreesen TD Henikoff S Loughney K A pairing-sensitive element that mediates trans-inactivation is associated with the Drosophila brown gene Genes Dev 1991, 5(3):331-340. 1848201
50. Holohan EE Kwong C Adryan B Bartkuhn M Herold M Renkawitz R Russell S White R CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex PLoS Genet 2007, 3(7):e112. 1904468 17616980
51. Adryan B Woerfel G Birch-Machin I Gao S Quick M Meadows L Russell S White R Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila Genome Biol 2007, 8(8):R167. 2374998 17705839
52. Mohan M Bartkuhn M Herold M Philippen A Heinl N Bardenhagen I Leers J White RA Renkawitz-Pohl R Saumweber H Renkawitz R The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning Embo J 2007, 26(19):4203-4214. 2230845 17805343
53. de Wit E Braunschweig U Greil F Bussemaker HJ van Steensel B Global chromatin domain organization of the Drosophila genome PLoS Genet 2008, 4(3):e1000045. 2274884 18369463
54. Negre N Hennetin J Sun LV Lavrov S Bellis M White KP Cavalli G Chromosomal distribution of PcG proteins during Drosophila development PLoS Biol 2006, 4(6):e170. 1440717 16613483
55. Bevis BJ Glick BS Rapidly maturing variants of the Discosoma red fluorescent protein (DsRed) Nat Biotechnol 2002, 20(1):83-87. 11753367
56. Galloni M Gyurkovics H Schedl P Karch F The bluetail transposon: evidence for independent cis-regulatory domains and domain boundaries in the bithorax complex Embo J 1993, 12(3):1087-1097. 413310 8384551
57. Hagstrom K Muller M Schedl P Fab-7 functions as a chromatin domain boundary to ensure proper segment specification by the Drosophila bithorax complex Genes Dev 1996, 10(24):3202-3215. 8985188
58. Schweinsberg S Hagstrom K Gohl D Schedl P Kumar RP Mishra R Karch F The enhancer-blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA-factor-binding sites Genetics 2004, 168(3):1371-1384. 1448804 15579691
59. Clemens JC Worby CA Simonson-Leff N Muda M Maehama T Hemmings BA Dixon JE Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways Proc Natl Acad Sci USA 2000, 97(12):6499-6503. 18635 10823906
60. Gerasimova TI Gdula DA Gerasimov DV Simonova O Corces VG A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation Cell 1995, 82(4):587-597. 7664338
61. Vlassov AV Li M Magdaleno S Improving In Vivo Delivery of siRNAs TechNote Newsletter 2008, 15(2):8.
62. Filippova GN Genetics and epigenetics of the multifunctional protein CTCF Curr Top Dev Biol 2008, 80:337-360. 17950379
63. Ling JQ Li T Hu JF Vu TH Chen HL Qiu XW Cherry AM Hoffman AR CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1 Science 2006, 312(5771):269-272. 16614224
64. Splinter E Heath H Kooren J Palstra RJ Klous P Grosveld F Galjart N de Laat W CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus Genes Dev 2006, 20(17):2349-2354. 1560409 16951251
65. Pai CY Lei EP Ghosh D Corces VG The centrosomal protein CP190 is a component of the gypsy chromatin insulator Mol Cell 2004, 16(5):737-748. 15574329
66. Benyajati C Mueller L Xu N Pappano M Gao J Mosammaparast M Conklin D Granok H Craig C Elgin S Multiple isoforms of GAGA factor, a critical component of chromatin structure Nucleic Acids Res 1997, 25(16):3345-3353. 146888 9241251
67. Parkhurst SM Harrison DA Remington MP Spana C Kelley RL Coyne RS Corces VG The Drosophila su(Hw) gene, which controls the phenotypic effect of the gypsy transposable element, encodes a putative DNA-binding protein Genes Dev 1988, 2(10):1205-1215. 2462523
68. Zhao K Hart CM Laemmli UK Visualization of chromosomal domains with boundary element-associated factor BEAF-32 Cell 1995, 81(6):879-889. 7781065
69. Holdridge C Dorsett D Repression of hsp70 heat shock gene transcription by the suppressor of hairy-wing protein of Drosophila melanogaster Mol Cell Biol 1991, 11(4):1894-1900. 359869 1900919
70. Aoki T Schweinsberg S Manasson J Schedl P A stage-specific factor confers Fab-7 boundary activity during early embryogenesis in Drosophila Mol Cell Biol 2008, 28(3):1047-1060. 2223392 18039839
71. Schneider I Cell lines derived from late embryonic stages of Drosophila melanogaster J Embryol Exp Morphol 1972, 27(2):353-365. 4625067