The orchestration of mammalian tissue morphogenesis through a series of coherent feed-forward loops

Journal of Biological Chemistry

Volumn 286, Issue 50, 2011, Pages 43259-43271

  Xie, Qing ^a   Cvekl, Ales ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSICAL MODEL; DNA-BINDING; EXPRESSION PATTERNS; FEEDFORWARD LOOPS; GENE REGULATORY NETWORKS; GENES ENCODING; LENS FIBERS; MAMMALIAN TISSUES; MULTIPLE REGIONS; OCULAR LENS; REGULATORY NETWORK; SPATIAL CONTROL; STRUCTURAL PROTEINS; SUB-CIRCUITS; TERMINAL DIFFERENTIATION; TRANSGENIC EXPRESSION;

BINDING SITES; MAMMALS; MORPHOLOGY; OPHTHALMOLOGY; TISSUE;

GENE EXPRESSION;

CRYSTALLIN; TRANSCRIPTION FACTOR C MAF; TRANSCRIPTION FACTOR PAX6;

ANIMAL TISSUE; ARTICLE; BINDING SITE; CHROMATIN; CONTROLLED STUDY; EMBRYO; EYE DEVELOPMENT; GENE REGULATORY NETWORK; LENS DEVELOPMENT; MORPHOGENESIS; MOUSE; MUTAGENESIS; NONHUMAN; PHENOTYPE; PIGMENT EPITHELIUM; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN EXPRESSION; TISSUE DIFFERENTIATION; TISSUE MORPHOGENESIS;

ANIMALS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; ELECTROPHORETIC MOBILITY SHIFT ASSAY; EYE PROTEINS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; GREEN FLUORESCENT PROTEINS; HOMEODOMAIN PROTEINS; LENS, CRYSTALLINE; MICE; MICE, TRANSGENIC; PAIRED BOX TRANSCRIPTION FACTORS; PROTO-ONCOGENE PROTEINS C-MAF; REPRESSOR PROTEINS; RETINAL PIGMENT EPITHELIUM; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 83355166954     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.264580     Document Type: Article

References (81)

1. Ali, R. R., and Sowden, J. C. (2011) Nature 472, 42-43
2. Eiraku, M., Takata, N., Ishibashi, H., Kawada, M., Sakakura, E., Okuda, S., Sekiguchi, K., Adachi, T., and Sasai, Y. (2011) Nature 472, 51-56
3. Yang, C., Yang, Y., Brennan, L., Bouhassira, E. E., Kantorow, M., and Cvekl, A. (2010) FASEB J. 24, 3274-3283
4. Davidson, E. H. (2010) Nature 468, 911-920
5. Peter, I. S., and Davidson, E. H. (2011) Cell 144, 970-985
6. Karlebach, G., and Shamir, R. (2008) Nat. Rev. Mol. Cell Biol. 9, 770-780
7. Olson, E. N. (2006) Science 313, 1922-1927
8. Orkin, S. H., Wang, J., Kim, J., Chu, J., Rao, S., Theunissen, T. W., Shen, X., and Levasseur, D. N. (2008) Cold Spring Harbor Symp. Quant. Biol. 73, 195-202
9. Shoval, O., and Alon, U. (2010) Cell 143, 326-e1
10. Chow, R. L., and Lang, R. A. (2001) Annu. Rev. Cell Dev. Biol. 17, 255-296
11. Gunhaga, L. (2011) Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 1193-1203
12. Medina-Martinez, O., and Jamrich, M. (2007) Development 134, 1455-1463
13. Ashery-Padan, R., Marquardt, T., Zhou, X., and Gruss, P. (2000) Genes Dev. 14, 2701-2711
14. Liu, W., Lagutin, O. V., Mende, M., Streit, A., and Oliver, G. (2006) EMBO J. 25, 5383-5395
15. Streit, A. (2004) Dev. Biol. 276, 1-15
16. Hill, R. E., Favor, J., Hogan, B. L., Ton, C. C., Saunders, G. F., Hanson, I. M., Prosser, J., Jordan, T., Hastie, N. D., and van Heyningen, V. (1991) Nature 354, 522-525
17. Hogan, B. L., Hirst, E. M., Horsburgh, G., and Hetherington, C. M. (1988) Development 103, 115-119
18. Quinn, J. C., West, J. D., and Hill, R. E. (1996) Genes Dev. 10, 435-446
19. Shaham, O., Smith, A. N., Robinson, M. L., Taketo, M. M., Lang, R. A., and Ashery-Padan, R. (2009) Development 136, 2567-2578
20. Collinson, J. M., Quinn, J. C., Buchanan, M. A., Kaufman, M. H., Wedden, S. E., West, J. D., and Hill, R. E. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 9688-9693
21. Cvekl, A., and Mitton, K. P. (2010) Heredity 105, 135-151
22. Czerny, T., and Busslinger, M. (1995) Mol. Cell. Biol. 15, 2858-2871
23. Kawauchi, S., Takahashi, S., Nakajima, O., Ogino, H., Morita, M., Nishizawa, M., Yasuda, K., and Yamamoto, M. (1999) J. Biol. Chem. 274, 19254-19260
24. Ring, B. Z., Cordes, S. P., Overbeek, P. A., and Barsh, G. S. (2000) Development 127, 307-317
25. Eychène, A., Rocques, N., and Pouponnot, C. (2008) Nat. Rev. Cancer 8, 683-693
26. Ise, W., Kohyama, M., Schraml, B. U., Zhang, T., Schwer, B., Basu, U., Alt, F. W., Tang, J., Oltz, E. M., Murphy, T. L., and Murphy, K. M. (2011) Nat. Immunol. 12, 536-543
27. Rani, A., Afzali, B., Kelly, A., Tewolde-Berhan, L., Hackett, M., Kanhere, A. S., Pedroza-Pacheco, I., Bowen, H., Jurcevic, S., Jenner, R. G., Cousins, D. J., Ragheb, J. A., Lavender, P., and John, S. (2011) J. Immunol. 187, 3721-3729
28. Kim, J. I., Ho, I. C., Grusby, M. J., and Glimcher, L. H. (1999) Immunity 10, 745-751
29. MacLean, H. E., Kim, J. I., Glimcher, M. J., Wang, J., Kronenberg, H. M., and Glimcher, L. H. (2003) Dev. Biol. 262, 51-63
30. Kusakabe, M., Hasegawa, K., Hamada, M., Nakamura, M., Ohsumi, T., Suzuki, H., Tran, M. T., Kudo, T., Uchida, K., Ninomiya, H., Chiba, S., and Takahashi, S. (2011) Blood 118, 1374-1385
31. Suzuki, A., Iida, S., Kato-Uranishi, M., Tajima, E., Zhan, F., Hanamura, I., Huang, Y., Ogura, T., Takahashi, S., Ueda, R., Barlogie, B., Shaughnessy, J., Jr., and Esumi, H. (2005) Oncogene 24, 6936-6944
32. Chi, N., and Epstein, J. A. (2002) Trends Genet 18, 41-47
33. van Heyningen, V., and Williamson, K. A. (2002) Hum. Mol. Genet. 11, 1161-1167
34. Graw, J. (2009) J. Genet. 88, 469-486
35. Jun, S., and Desplan, C. (1996) Development 122, 2639-2650
36. Singh, S., Mishra, R., Arango, N. A., Deng, J. M., Behringer, R. R., and Saunders, G. F. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 6812-6815
37. Kozmik, Z., Czerny, T., and Busslinger, M. (1997)EMBOJ. 16, 6793-6803
38. Epstein, J., Cai, J., Glaser, T., Jepeal, L., and Maas, R. (1994) J. Biol. Chem. 269, 8355-8361
39. Epstein, J. A., Glaser, T., Cai, J., Jepeal, L., Walton, D. S., and Maas, R. L. (1994) Genes Dev. 8, 2022-2034
40. Xu, H. E., Rould, M. A., Xu, W., Epstein, J. A., Maas, R. L., and Pabo, C. O. (1999) Genes Dev. 13, 1263-1275
41. Cvekl, A., and Duncan, M. K. (2007) Prog. Retin. Eye Res. 26, 555-597
42. Götz, M., and Huttner, W. B. (2005) Nat. Rev. Mol. Cell Biol. 6, 777-788
43. Nomura, T., Haba, H., and Osumi, N. (2007) Dev. Growth Differ. 49, 683-690
44. Osumi, N., Shinohara, H., Numayama-Tsuruta, K., and Maekawa, M. (2008) Stem Cells 26, 1663-1672
45. Decker, T., Pasca di Magliano, M., McManus, S., Sun, Q., Bonifer, C., Tagoh, H., and Busslinger, M. (2009) Immunity 30, 508-520
46. Schebesta, A., McManus, S., Salvagiotto, G., Delogu, A., Busslinger, G. A., and Busslinger, M. (2007) Immunity 27, 49-63
47. Berger, M. F., Badis, G., Gehrke, A. R., Talukder, S., Philippakis, A. A., Peña-Castillo, L., Alleyne, T. M., Mnaimneh, S., Botvinnik, O. B., Chan, E. T., Khalid, F., Zhang, W., Newburger, D., Jaeger, S. A., Morris, Q. D., Bulyk, M. L., and Hughes, T. R. (2008) Cell 133, 1266-1276
48. Rowan, S., Siggers, T., Lachke, S. A., Yue, Y., Bulyk, M. L., and Maas, R. L. (2010) Genes Dev. 24, 980-985
49. Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., Gifford, D. K., Melton, D. A., Jaenisch, R., and Young, R. A. (2005) Cell 122, 947-956
50. Yang, Y., Stopka, T., Golestaneh, N., Wang, Y., Wu, K., Li, A., Chauhan, B. K., Gao, C. Y., Cveklová, K., Duncan, M. K., Pestell, R. G., Chepelinsky, A. B., Skoultchi, A. I., and Cvekl, A. (2006) EMBO J. 25, 2107-2118
51. Chauhan, B. K., Yang, Y., Cveklová, K., and Cvekl, A. (2004) Nucleic Acids Res. 32, 1696-1709
52. Duncan, M. K., Kozmik, Z., Cveklova, K., Piatigorsky, J., and Cvekl, A. (2000) J. Cell Sci. 113, 3173-3185
53. Grindley, J. C., Davidson, D. R., and Hill, R. E. (1995) Development 121, 1433-1442
54. Walther, C., and Gruss, P. (1991) Development 113, 1435-1449
55. Shimoda, Y., Tajima, Y., Osanai, T., Katsume, A., Kohara, M., Kudo, T., Narimatsu, H., Takashima, N., Ishii, Y., Nakamura, S., Osumi, N., and Sanai, Y. (2002) J. Biol. Chem. 277, 2033-2039
56. Visel, A., Carson, J., Oldekamp, J., Warnecke, M., Jakubcakova, V., Zhou, X., Shaw, C. A., Alvarez-Bolado, G., and Eichele, G. (2007) PLoS Genet. 3, 1867-1883
57. Wolf, L. V., Yang, Y., Wang, J., Xie, Q., Braunger, B., Tamm, E. R., Zavadil, J., and Cvekl, A. (2009) PLoS ONE 4, e4159
58. Djordjevic, M. (2007) Biomol. Eng. 24, 179-189
59. Chauhan, B. K., Yang, Y., Cveklová, K., and Cvekl, A. (2004) Invest. Ophthalmol. Vis. Sci. 45, 385-392
60. Yang, Y., Chauhan, B. K., Cveklova, K., and Cvekl, A. (2004) J. Mol. Biol. 344, 351-368
61. Kozmikova, I., Smolikova, J., Vlcek, C., and Kozmik, Z. (2011) PLoSONE6, e14650
62. Swiers, G., Patient, R., and Loose, M. (2006) Dev. Biol. 294, 525-540
63. Aota, S., Nakajima, N., Sakamoto, R., Watanabe, S., Ibaraki, N., and Okazaki, K. (2003) Dev. Biol. 257, 1-13
64. Chen, Q., Dowhan, D. H., Liang, D., Moore, D. D., and Overbeek, P. A. (2002) J. Biol. Chem. 277, 24081-24089
65. Donner, A. L., Episkopou, V., and Maas, R. L. (2007) Dev. Biol. 303, 784-799
66. Bateman, E. (1998) Prog. Nucleic Acid Res. Mol. Biol. 60, 133-168
67. Sakai, M., Serria, M. S., Ikeda, H., Yoshida, K., Imaki, J., and Nishi, S. (2001) Nucleic Acids Res. 29, 1228-1237
68. Dressler, G. R. (2009) Organogenesis 5, 73-82
69. Dressler, G. R. (2009) Development 136, 3863-3874
70. Civil, A., van Genesen, S. T., and Lubsen, N. H. (2002) Nucleic Acids Res. 30, 975-982
71. Liu, S., and Piatigorsky, J. (2011) PLoS ONE 6, e17904
72. Fujimoto, M., Izu, H., Seki, K., Fukuda, K., Nishida, T., Yamada, S., Kato, K., Yonemura, S., Inouye, S., and Nakai, A. (2004) EMBO J. 23, 4297-4306
73. Nishiguchi, S., Wood, H., Kondoh, H., Lovell-Badge, R., and Episkopou, V. (1998) Genes Dev. 12, 776-781
74. Wigle, J. T., Chowdhury, K., Gruss, P., and Oliver, G. (1999) Nat. Genet. 21, 318-322
75. Lachke, S. A., Alkuraya, F. S., Kneeland, S. C., Ohn, T., Aboukhalil, A., Howell, G. R., Saadi, I., Cavallesco, R., Yue, Y., Tsai, A. C., Nair, K. S., Cosma, M. I., Smith, R. S., Hodges, E., Alfadhli, S. M., Al-Hajeri, A., Shamseldin, H. E., Behbehani, A., Hannon, G. J., Bulyk, M. L., Drack, A. V., Anderson, P. J., John, S. W., and Maas, R. L. (2011) Science 331, 1571-1576
76. Horwitz, J. (2003) Exp. Eye Res. 76, 145-153
77. Bassnett, S. (2009) Exp. Eye Res. 88, 133-139
78. Gordân, R., Hartemink, A. J., and Bulyk, M. L. (2009) Genome Res. 19, 2090-2100
79. Harada, T., Harada, C., and Parada, L. F. (2007) Genes Dev. 21, 367-378
80. Ninkovic, J., Pinto, L., Petricca, S., Lepier, A., Sun, J., Rieger, M. A., Schroeder, T., Cvekl, A., Favor, J., and Götz, M. (2010) Neuron 68, 682-694
81. Herold, S., Jagasia, R., Merz, K., Wassmer, K., and Lie, D. C. (2011) Mol. Cell Neurosci. 46, 79-88