A functionally conserved boundary element from the mouse HoxD locus requires GAGA factor in Drosophila

Development

Volumn 137, Issue 24, 2010, Pages 4239-4247

  Vasanthi, Dasari ^a   Anant, Mamidi ^a   Srivastava, Surabhi ^a   Mishra, Rakesh K ^a  

^a CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

Chromatin domain boundary; Drosophila; GAGA factor; HoxD

Indexed keywords

GAGA FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DROSOPHILA; EMBRYO; GENE; GENE CONTROL; GENE FUNCTION; GENE LOCUS; GENE SEQUENCE; GENETIC CONSERVATION; HOX GENE; HUMAN; HUMAN CELL; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TRITHORAX LIKE GENE;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; CELL LINE, TUMOR; CHROMATIN IMMUNOPRECIPITATION; DNA-BINDING PROTEINS; DROSOPHILA; DROSOPHILA PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HOMEODOMAIN PROTEINS; HUMANS; INTEGRASES; MICE; POLYMERASE CHAIN REACTION; TRANSCRIPTION FACTORS;

MAMMALIA; VERTEBRATA;

EID: 78650183503     PISSN: 09501991     EISSN: 14779129     Source Type: Journal    
DOI: 10.1242/dev.058701     Document Type: Article

References (47)

1. 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.
2. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S. and Haussler, D. (2004). Ultraconserved elements in the human genome. Science 304, 1321-1325.
3. 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.
4. 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.
5. 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.
6. Chung, J. H., Whiteley, M. and Felsenfeld, G. (1993). 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 74, 505-514.
7. Deschamps, J., van den Akker, E., Forlani, S., De Graaff, W., Oosterveen, T., Roelen, B. and Roelfsema, J. (1999). Initiation, establishment and maintenance of Hox gene expression patterns in the mouse. Int. J. Dev. Biol. 43, 635-650.
8. 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.
9. Farkas, G., Gausz, J., Galloni, M., Reuter, G., Gyurkovics, H. and Karch, F. (1994). The Trithorax-like gene encodes the Drosophila GAGA factor. Nature 371, 806-808.
10. Featherstone, M. S., Baron, A., Gaunt, S. J., Mattei, M. G. and Duboule, D. (1988). Hox-5.1 defines a homeobox-containing gene locus on mouse chromosome 2. Proc. Natl. Acad. Sci. USA 85, 4760-4764.
11. 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.
12. Garcia-Fernandez, J. (2005). The genesis and evolution of homeobox gene clusters. Nat. Rev. Genet. 6, 881-892.
13. Gaunt, S. J., Krumlauf, R. and Duboule, D. (1989). Mouse homeo-genes within a subfamily, Hox-1.4, -2.6 and -5.1, display similar anteroposterior domains of expression in the embryo, but show stage- and tissue-dependent differences in their regulation. Development 107, 131-141.
14. Graham, A., Papalopulu, N. and Krumlauf, R. (1989). The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57, 367-378.
15. Grossniklaus, U., Bellen, H. J., Wilson, C. and Gehring, W. J. (1989). Pelement- mediated enhancer detection applied to the study of oogenesis in Drosophila. Development 107, 189-200.
16. 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.
17. 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.
18. Iqbal, H. and Mishra, R. K. (2007). Chromatin domain boundaries: defining the functional domains in genome. Proc. Indian Natl. Sci. Acad. 73, 239-253.
19. Izpisua-Belmonte, J. C., Falkenstein, H., Dolle, P., Renucci, A. and Duboule, D. (1991). Murine genes related to the Drosophila AbdB homeotic genes are sequentially expressed during development of the posterior part of the body. EMBO J. 10, 2279-2289.
20. Karch, F., Galloni, M., Sipos, L., Gausz, J., Gyurkovics, H. and Schedl, P. (1994). Mcp and Fab-7: molecular analysis of putative boundaries of cis-regulatory domains in the bithorax complex of Drosophila melanogaster. Nucleic Acids Res. 22, 3138-3146.
21. Kessel, M. and Gruss, P. (1990). Murine developmental control genes. Science 249, 374-379.
22. Kmita, M., Kondo, T. and Duboule, D. (2000a). Targeted inversion of a polar silencer within the HoxD complex re-allocates domains of enhancer sharing. Nat. Genet. 26, 451-454.
23. Kmita, M., van Der Hoeven, F., Zakany, J., Krumlauf, R. and Duboule, D. (2000b). Mechanisms of Hox gene colinearity: transposition of the anterior Hoxb1 gene into the posterior HoxD complex. Genes Dev. 14, 198-211.
24. Kmita, M., Tarchini, B., Duboule, D. and Herault, Y. (2002). Evolutionary conserved sequences are required for the insulation of the vertebrate Hoxd complex in neural cells. Development 129, 5521-5528.
25. Krumlauf, R. (1994). Hox genes in vertebrate development. Cell 78, 191-201.
26. Lewis, E. B. (1978). A gene complex controlling segmentation in Drosophila. Nature 276, 565-570.
27. Li, J., Liang, V. C., Sedgwick, T., Wong, J. and Shi, Y. B. (1998). Unique organization and involvement of GAGA factors in transcriptional regulation of the Xenopus stromelysin-3 gene. Nucleic Acids Res. 26, 3018-3025.
28. Matharu, N. K., Hussain, T., Sankaranarayanan, R. and Mishra, R. K. (2010). Vertebrate homologue of Drosophila GAGA factor. J. Mol. Biol. 400, 434-447.
29. McGinnis, W. and Krumlauf, R. (1992). Homeobox genes and axial patterning. Cell 68, 283-302.
30. McGinnis, W., Garber, R. L., Wirz, J., Kuroiwa, A. and Gehring, W. J. (1984a). A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans. Cell 37, 403-408.
31. McGinnis, W., Hart, C. P., Gehring, W. J. and Ruddle, F. H. (1984b). Molecular cloning and chromosome mapping of a mouse DNA sequence homologous to homeotic genes of Drosophila. Cell 38, 675-680.
32. 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.
33. Mihaly, J., Hogga, I., Barges, S., Galloni, M., Mishra, R. K., Hagstrom, K., Muller, M., Schedl, P., Sipos, L., Gausz, J. et al. (1998). Chromatin domain boundaries in the Bithorax complex. Cell. Mol. Life Sci. 54, 60-70.
34. Mishra, K., Chopra, V. S., Srinivasan, A. and Mishra, R. K. (2003). Trl-GAGA directly interacts with lola like and both are part of the repressive complex of Polycomb group of genes. Mech. Dev. 120, 681.
35. Mishra, R. K. and Karch, F. (1999). Boundaries that demarcate structural and functional domains of chromatin. J. Biosci. 24, 377-399.
36. 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.
37. 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.
38. Nakayama, T., Nishioka, K., Dong, Y. X., Shimojima, T. and Hirose, S. (2007). Drosophila GAGA factor directs histone H3.3 replacement that prevents the heterochromatin spreading. Genes Dev. 21, 552-561.
39. Negre, N., Brown, C. D., Shah, P. K., Kheradpour, P., Morrison, C. A., Henikoff, J. G., Feng, X., Ahmad, K., Russell, S., White, R. A. et al. (2010). A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 6, e1000814.
40. 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.
41. Ringrose, L. and Paro, R. (2004). Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413-443.
42. Sabarinadh, C., Subramanian, S., Tripathi, A. and Mishra, R. K. (2004). Extreme conservation of noncoding DNA near HoxD complex of vertebrates. BMC Genomics 5, 75.
43. Schweinsberg, S. E. and Schedl, P. (2004). Developmental modulation of Fab-7 boundary function. Development 131, 4743-4749.
44. 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.
45. 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.
46. Yamagishi, T., Ozawa, M., Ohtsuka, C., Ohyama-Goto, R. and Kondo, T. (2007). Evx2-hoxd13 intergenic region restricts enhancer association to hoxd13 promoter. PLoS ONE 2, e175.
47. Yuan, J. S., Reed, A., Chen, F. and Stewart, C. N. J. (2006). Statistical analysis of real-time PCR data. BMC Bioinformatics 7, 85.