Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae

Nucleic Acids Research

Volumn 41, Issue 2, 2013, Pages 804-816

  Ahanger, Sajad H ^a   Srinivasan, Arumugam ^b   Vasanthi, Dasari ^b   Shouche, Yogesh S ^a   Mishra, Rakesh K ^b  

^a NATIONAL CENTRE FOR CELL SCIENCE   (India)

^b CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ANOPHELES GAMBIAE; ARTICLE; BINDING SITE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EMBRYO; FEMALE; GENE CLUSTER; GENE FUNCTION; GENE LOCUS; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC REGULATION; HOX GENE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; ANOPHELES GAMBIAE; CELLS, CULTURED; DROSOPHILA; EVOLUTION, MOLECULAR; GENES, HOMEOBOX; INSULATOR ELEMENTS; MUTATION; SEQUENCE ANALYSIS, DNA;

ANOPHELES GAMBIAE; HEXAPODA;

EID: 84875435607     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1178     Document Type: Article

References (66)

1. Kaufman, T.C., Lewis, R. and Wakimoto, B. (1980) Cytogenetic analysis of chromosome 3 in Drosophila melanogaster: the homoeotic gene complex in polytene chromosome interval 84a-B. Genetics, 94, 115-133. (Pubitemid 10037865)
2. Lewis, E.B. (1978) A gene complex controlling segmentation in Drosophila. Nature, 276, 565-570. (Pubitemid 9087758)
3. Duboule, D. and Dolle, P. (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J., 8, 1497-1505. (Pubitemid 19274377)
4. Duboule, D. and Morata, G. (1994) Colinearity and functional hierarchy among genes of the homeotic complexes. Trends Genet., 10, 358-364. (Pubitemid 24305375)
5. Krumlauf, R. (1994) Hox genes in vertebrate development. Cell, 78, 191-201. (Pubitemid 24241088)
6. McGinnis, W. and Krumlauf, R. (1992) Homeobox genes and axial patterning. Cell, 68, 283-302.
7. Lawrence, P.A. and Morata, G. (1994) Homeobox genes: their function in Drosophila segmentation and pattern formation. Cell, 78, 181-189. (Pubitemid 24241087)
8. Von Allmen, G., Hogga, I., Spierer, A., Karch, F., Bender, W., Gyurkovics, H. and Lewis, E. (1996) Splits in fruitfly Hox gene complexes. Nature, 380, 116. (Pubitemid 26085874)
9. Lewis, E.B., Pfeiffer, B.D., Mathog, D.R. and Celniker, S.E. (2003) Evolution of the homeobox complex in the Diptera. Curr. Biol., 13, R587-R588. (Pubitemid 36953287)
10. Yasukochi, Y., Ashakumary, L.A., Wu, C., Yoshido, A., Nohata, J., Mita, K. and Sahara, K. (2004) Organization of the Hox gene cluster of the silkworm, Bombyx mori: a split of the Hox cluster in a non-Drosophila insect. Dev. Genes Evol., 214, 606-614. (Pubitemid 40017354)
11. Chai, C.L., Zhang, Z., Huang, F.F., Wang, X.Y., Yu, Q.Y., Liu, B.B., Tian, T., Xia, Q.Y., Lu, C. and Xiang, Z.H. (2008) A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori. Insect Biochem. Mol. Biol., 38, 1111-1120.
12. Denell, R.E., Brown, S.J. and Beeman, R.W. (1996) Evolution of the organization and function of insect homeotic complexes. Semin. Cell Dev. Biol., 527-538. (Pubitemid 126320522)
13. Shippy, T.D., Ronshaugen, M., Cande, J., He, J., Beeman, R.W., Levine, M., Brown, S.J. and Denell, R.E. (2008) Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters. Dev. Genes Evol., 218, 127-139. (Pubitemid 351513913)
14. Walldorf, U., Binner, P. and Fleig, R. (2000) Hox genes in the honey bee Apis mellifera. Dev. Genes Evol., 210, 483-492.
15. Ferrier, D.E. and Akam, M. (1996) Organization of the Hox gene cluster in the grasshopper, Schistocerca gregaria. Proc. Natl Acad. Sci. USA, 93, 13024-13029. (Pubitemid 26382763)
16. Devenport, M.P., Blass, C. and Eggleston, P. (2000) Characterization of the Hox gene cluster in the malaria vector mosquito, Anopheles gambiae. Evol. Dev., 2, 326-339.
17. Powers, T.P., Hogan, J., Ke, Z., Dymbrowski, K., Wang, X., Collins, F.H. and Kaufman, T.C. (2000) Characterization of the Hox cluster from the mosquito Anopheles gambiae (Diptera: Culicidae). Evol. Dev., 2, 311-325.
18. Duboule, D. (2007) The rise and fall of Hox gene clusters. Development, 134, 2549-2560. (Pubitemid 47225952)
19. Randazzo, F.M., Seeger, M.A., Huss, C.A., Sweeney, M.A., Cecil, J.K. and Kaufman, T.C. (1993) Structural changes in the antennapedia complex of Drosophila pseudoobscura. Genetics, 134, 319-330. (Pubitemid 23127232)
20. Maeda, R.K. and Karch, F. (2006) The ABC of the BX-C: the bithorax complex explained. Development, 133, 1413-1422. (Pubitemid 43732955)
21. Barges, S., Mihaly, J., Galloni, M., Hagstrom, K., Muller, M., Shanower, G., Schedl, P., Gyurkovics, H. and Karch, F. (2000) 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, 127, 779-790. (Pubitemid 30129024)
22. Galloni, M., Gyurkovics, H., Schedl, P. and Karch, F. (1993) The bluetail transposon: evidence for independent cis-regulatory domains and domain boundaries in the bithorax complex. EMBO J., 12, 1087-1097. (Pubitemid 23095858)
23. Hogga, I., Mihaly, J., Barges, S. and Karch, F. (2001) Replacement of Fab-7 by the gypsy or scs insulator disrupts long-distance regulatory interactions in the Abd-B gene of the bithorax complex. Mol. Cell, 8, 1145-1151. (Pubitemid 34031816)
24. Mihaly, J., Hogga, I., Gausz, J., Gyurkovics, H. and Karch, F. (1997) In situ dissection of the Fab-7 region of the bithorax complex into a chromatin domain boundary and a Polycomb-response element. Development, 124, 1809-1820. (Pubitemid 27248347)
25. Gyurkovics, H., Gausz, J., Kummer, J. and Karch, F. (1990) A new homeotic mutation in the Drosophila bithorax complex removes a boundary separating two domains of regulation. EMBO J., 9, 2579-2585.
26. Bolshakov, V.N., Topalis, P., Blass, C., Kokoza, E., della Torre, A., Kafatos, F.C. and Louis, C. (2002) A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae. Genome Res., 12, 57-66. (Pubitemid 34065589)
27. Bender, W., Akam, M., Karch, F., Beachy, P.A., Peifer, M., Spierer, P., Lewis, E.B. and Hogness, D.S. (1983) Molecular genetics of the bithorax complex in Drosophila melanogaster. Science, 221, 23-29. (Pubitemid 13061683)
28. Kaufman, T.C., Seeger, M.A. and Olsen, G. (1990) Molecular and genetic organization of the antennapedia gene complex of Drosophila melanogaster. Adv. Genet., 27, 309-362.
29. Seeger, M.A., Haffley, L. and Kaufman, T.C. (1988) Characterization of amalgam: a member of the immunoglobulin superfamily from Drosophila. Cell, 55, 589-600.
30. Schoborg, T.A. and Labrador, M. (2010) The phylogenetic distribution of non-CTCF insulator proteins is limited to insects and reveals that BEAF-32 is Drosophila lineage specific. J. Mol. Evol., 70, 74-84.
31. Srinivasan, A. and Mishra, R.K. (2012) Chromatin domain boundary element search tool for Drosophila. Nucleic Acids Res., 40, 4385-4395.
32. Starr, M.O., Ho, M.C., Gunther, E.J., Tu, Y.K., Shur, A.S., Goetz, S.E., Borok, M.J., Kang, V. and Drewell, R.A. (2011) Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs. Dev. Biol., 359, 290-302.
33. Vasanthi, D., Anant, M., Srivastava, S. and Mishra, R.K. (2010) A functionally conserved boundary element from the mouse HoxD locus requires GAGA factor in Drosophila. Development, 137, 4239-4247.
34. Hagstrom, K., Muller, M. and Schedl, P. (1996) Fab-7 functions as a chromatin domain boundary to ensure proper segment specification by the Drosophila bithorax complex. Genes Dev., 10, 3202-3215. (Pubitemid 27020547)
35. Siegal, M.L. and Hartl, D.L. (1996) Transgene coplacement and high efficiency site-specific recombination with the Cre/loxP system in Drosophila. Genetics, 144, 715-726. (Pubitemid 26325862)
36. Gray, C.E. and Coates, C.J. (2005) Cloning and characterization of cDNAs encoding putative CTCFs in the mosquitoes, Aedes aegypti and Anopheles gambiae. BMC Mol. Biol., 6, 16.
37. Belozerov, V.E., Majumder, P., Shen, P. and Cai, H.N. (2003) A novel boundary element may facilitate independent gene regulation in the Antennapedia complex of Drosophila. EMBO J., 22, 3113-3121. (Pubitemid 36758631)
38. Recillas-Targa, F., Bell, A.C. and Felsenfeld, G. (1999) Positional enhancer-blocking activity of the chicken beta-globin insulator in transiently transfected cells. Proc. Natl Acad. Sci. USA, 96, 14354-14359. (Pubitemid 30000654)
39. Recillas-Targa, F., Pikaart, M.J., Burgess-Beusse, B., Bell, A.C., Litt, M.D., West, A.G., Gaszner, M. and Felsenfeld, G. (2002) Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities. Proc. Natl Acad. Sci. USA, 99, 6883-6888. (Pubitemid 34526227)
40. Yao, S., Osborne, C.S., Bharadwaj, R.R., Pasceri, P., Sukonnik, T., Pannell, D., Recillas-Targa, F., West, A.G. and Ellis, J. (2003) Retrovirus silencer blocking by the cHS4 insulator is CTCF independent. Nucleic Acids Res., 31, 5317-5323. (Pubitemid 37441899)
41. Li, M., Belozerov, V.E. and Cai, H.N. (2008) Analysis of chromatin boundary activity in Drosophila cells. BMC Mol. Biol., 9, 109.
42. Wittkopp, P.J. (2006) Evolution of cis-regulatory sequence and function in Diptera. Heredity, 97, 139-147. (Pubitemid 44289675)
43. Poux, S., Melfi, R. and Pirrotta, V. (2001) Establishment of Polycomb silencing requires a transient interaction between PC and ESC. Genes Dev., 15, 2509-2514. (Pubitemid 32937861)
44. Leibovitch, B.A., Lu, Q., Benjamin, L.R., Liu, Y., Gilmour, D.S. and Elgin, S.C. (2002) GAGA factor and the TFIID complex collaborate in generating an open chromatin structure at the Drosophila melanogaster hsp26 promoter. Mol. Cell. Biol., 22, 6148-6157. (Pubitemid 34857835)
45. Ohtsuki, S. and Levine, M. (1998) GAGA mediates the enhancer blocking activity of the eve promoter in the Drosophila embryo. Genes Dev., 12, 3325-3330. (Pubitemid 28520980)
46. Chopra, V.S., Srinivasan, A., Kumar, R.P., Mishra, K., Basquin, D., Docquier, M., Seum, C., Pauli, D. and Mishra, R.K. (2008) Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3. Dev. Biol., 317, 660-670.
47. Mohan, M., Bartkuhn, M., Herold, M., Philippen, A., Heinl, N., Bardenhagen, I., Leers, J., White, R.A., Renkawitz-Pohl, R., Saumweber, H. et al. (2007) The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning. EMBO J., 26, 4203-4214. (Pubitemid 47525162)
48. Pai, C.Y., Lei, E.P., Ghosh, D. and Corces, V.G. (2004) The centrosomal protein CP190 is a component of the gypsy chromatin insulator. Mol Cell, 16, 737-748. (Pubitemid 39586532)
49. Holohan, E.E., Kwong, C., Adryan, B., Bartkuhn, M., Herold, M., Renkawitz, R., Russell, S. and White, R. (2007) CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex. PLoS Genet., 3, e112.
50. Geyer, P.K. and Corces, V.G. (1992) DNA position-specific repression of transcription by a Drosophila zinc finger protein. Genes Dev., 6, 1865-1873.
51. Gaszner, M., Vazquez, J. and Schedl, P. (1999) The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer-promoter interaction. Genes Dev., 13, 2098-2107. (Pubitemid 29407350)
52. Zhao, K., Hart, C.M. and Laemmli, U.K. (1995) Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell, 81, 879-889.
53. Gerasimova, T.I., Gdula, D.A., Gerasimov, D.V., Simonova, O. and Corces, V.G. (1995) A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation. Cell, 82, 587-597.
54. Moon, H., Filippova, G., Loukinov, D., Pugacheva, E., Chen, Q., Smith, S.T., Munhall, A., Grewe, B., Bartkuhn, M., Arnold, R. et al. (2005) CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator. EMBO Rep., 6, 165-170. (Pubitemid 40309414)
55. Bell, A.C., West, A.G. and Felsenfeld, G. (1999) The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell, 98, 387-396. (Pubitemid 29380573)
56. Matharu, N.K., Hussain, T., Sankaranarayanan, R. and Mishra, R.K. (2010) Vertebrate homologue of Drosophila GAGA factor. J. Mol. Biol., 400, 434-447.
57. Capelson, M. and Corces, V.G. (2005) The ubiquitin ligase dTopors directs the nuclear organization of a chromatin insulator. Mol. Cell, 20, 105-116. (Pubitemid 41396566)
58. Ghosh, D., Gerasimova, T.I. and Corces, V.G. (2001) Interactions between the Su(Hw) and Mod(mdg4) proteins required for gypsy insulator function. EMBO J., 20, 2518-2527. (Pubitemid 32452870)
59. Lei, E.P. and Corces, V.G. (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat. Genet., 38, 936-941. (Pubitemid 44141664)
60. Moshkovich, N., Nisha, P., Boyle, P.J., Thompson, B.A., Dale, R.K. and Lei, E.P. (2011) RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev., 25, 1686-1701.
61. Mishra, R.K., Mihaly, J., Barges, S., Spierer, A., Karch, F., Hagstrom, K., Schweinsberg, S.E. and Schedl, P. (2001) The iab-7 polycomb response element maps to a nucleosome-free region of chromatin and requires both GAGA and pleiohomeotic for silencing activity. Mol. Cell. Biol., 21, 1311-1318. (Pubitemid 32114978)
62. Okada, M. and Hirose, S. (1998) Chromatin remodeling mediated by Drosophila GAGA factor and ISWI activates fushi tarazu gene transcription in vitro. Mol. Cell. Biol., 18, 2455-2461. (Pubitemid 28183415)
63. Schweinsberg, S., Hagstrom, K., Gohl, D., Schedl, P., Kumar, R.P., Mishra, R. and Karch, F. (2004) The enhancer-blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA-factor-binding sites. Genetics, 168, 1371-1384. (Pubitemid 40007353)
64. Gerasimova, T.I., Lei, E.P., Bushey, A.M. and Corces, V.G. (2007) Coordinated control of dCTCF and gypsy chromatin insulators in Drosophila. Mol. Cell, 28, 761-772. (Pubitemid 350217054)
65. Bushey, A.M., Ramos, E. and Corces, V.G. (2009) Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev., 23, 1338-1350.
66. Sultana, H., Verma, S. and Mishra, R.K. (2011) A BEAF dependent chromatin domain boundary separates myoglianin and eyeless genes of Drosophila melanogaster. Nucleic Acids Res., 39, 3543-3557.