Epigenetic regulatory mechanisms distinguish retinoic acid-mediated transcriptional responses in stem cells and fibroblasts

Journal of Biological Chemistry

Volumn 285, Issue 19, 2010, Pages 14534-14548

  Kashyap, Vasundhra ^a   Gudas, Lorraine J ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COACTIVATORS; COMPLEX MECHANISMS; CPG ISLANDS; CYP26A1; EPIGENETIC MODIFICATION; GENE REPRESSION; HETERODIMERS; LOW LEVEL; MEDIATED TRANSCRIPTION; MOUSE EMBRYONIC FIBROBLASTS; POLYCOMB; PROMOTER REGION; RECEPTOR INTERACTION; REGULATORY MECHANISM; RESPONSE ELEMENTS; RETINOIC ACIDS; RETINOID X RECEPTOR; RNA POLYMERASE II; TARGET GENES; TRANSCRIPTIONAL REGULATOR; TRANSCRIPTIONAL RESPONSE; VITAMIN A;

ACETYLATION; ACIDS; CELL CULTURE; FIBROBLASTS; GENES; PROTEINS; RNA; TISSUE; TRANSCRIPTION;

STEM CELLS;

CYTOCHROME P450 26A1; DNA; POLYCOMB GROUP PROTEIN; PROTEIN P300; RETINOIC ACID; RETINOIC ACID RECEPTOR; RETINOIC ACID RECEPTOR ALPHA; RETINOIC ACID RECEPTOR BETA; RETINOIC ACID RECEPTOR GAMMA; RETINOID X RECEPTOR; RNA POLYMERASE II; STEROID RECEPTOR COACTIVATOR 3; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR HOXA1; UNCLASSIFIED DRUG;

ACETYLATION; ANIMAL CELL; ARTICLE; CELL CULTURE; CELL IMMORTALIZATION; CHROMATIN; CONTROLLED STUDY; CPG ISLAND; DNA MODIFICATION; DNA RESPONSIVE ELEMENT; EMBRYO; EMBRYO CELL; EMBRYONAL CARCINOMA STEM CELL; EPIGENETICS; FIBROBLAST; GENE REPRESSION; GENETIC TRANSCRIPTION; METHYLATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN TRANSPORT; RECEPTOR BINDING; REGULATORY MECHANISM; STEM CELL; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ANIMALS; BALB 3T3 CELLS; BLOTTING, WESTERN; CELLS, CULTURED; CHROMATIN IMMUNOPRECIPITATION; CYTOCHROME P-450 ENZYME SYSTEM; DNA METHYLATION; E1A-ASSOCIATED P300 PROTEIN; ELECTROPHORETIC MOBILITY SHIFT ASSAY; EMBRYO, MAMMALIAN; EMBRYONAL CARCINOMA STEM CELLS; EPIGENESIS, GENETIC; FIBROBLASTS; GENE EXPRESSION REGULATION; HISTONES; HOMEODOMAIN PROTEINS; MICE; MICE, INBRED BALB C; PROMOTER REGIONS, GENETIC; RECEPTORS, RETINOIC ACID; RESPONSE ELEMENTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA POLYMERASE II; RNA, MESSENGER; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ACTIVATION; TRETINOIN;

EID: 77951992661     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M110.115345     Document Type: Article

References (88)

1. Niederreither, K., and Dollé, P. (2008) Nat. Rev. Genet. 9, 541-553
2. Gudas, L. J. (1994) J. Biol. Chem. 269, 15399-15402
3. Blomhoff, R., and Blomhoff, H. K. (2006) J. Neurobiol. 66, 606-630
4. Bastien, J., and Rochette-Egly, C. (2004) Gene 328, 1-16
5. Kastner, P., Mark, M., Ghyselinck, N., Krezel, W., Dupé, V., Grondona, J. M., and Chambon, P. (1997) Development 124, 313-326
6. Matt, N., Ghyselinck, N. B., Wendling, O., Chambon, P., and Mark, M. (2003) Development 130, 2083-2093
7. Vasios, G. W., Gold, J. D., Petkovich, M., Chambon, P., and Gudas, L. J. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 9099-9103
8. Langston, A. W., and Gudas, L. J. (1992) Mech. Dev. 38, 217-227
9. de Thé, H., Vivanco-Ruiz, M. M., Tiollais, P., Stunnenberg, H., and Dejean, A. (1990) Nature 343, 177-180
10. Leid, M., Kastner, P., and Chambon, P. (1992) Trends Biochem. Sci. 17, 427-433
11. Chambon, P. (1996) FASEB J. 10, 940-954
12. Mark, M., Ghyselinck, N. B., and Chambon, P. (2006) Annu. Rev. Pharmacol. Toxicol. 46, 451-480
13. Boylan, J. F., Lohnes, D., Taneja, R., Chambon, P., and Gudas, L. J. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 9601-9605
14. Zhuang, Y., Faria, T. N., Chambon, P., and Gudas, L. J. (2003) Mol. Cancer Res. 1, 619-630
15. Dilworth, F. J., and Chambon, P. (2001) Oncogene 20, 3047-3054
16. Kurokawa, R., Söderström, M., Hörlein, A., Halachmi, S., Brown, M., Rosenfeld, M. G., and Glass, C. K. (1995) Nature 377, 451-454
17. Chen, J. D., and Evans, R. M. (1995) Nature 377, 454-457
18. Nagy, L., and Schwabe, J. W. (2004) Trends Biochem. Sci 29, 317-324
19. Glass, C. K., and Rosenfeld, M. G. (2000) Genes Dev. 14, 121-141
20. Leo, C., and Chen, J. D. (2000) Gene 245, 1-11
21. Wei, L. N. (2003) Annu. Rev. Pharmacol. Toxicol. 43, 47-72
22. Spencer, T. E., Jenster, G., Burcin, M. M., Allis, C. D., Zhou, J., Mizzen, C. A., McKenna, N. J., Onate, S. A., Tsai, S. Y., Tsai, M. J., and O'Malley, B. W. (1997) Nature 389, 194-198
23. McKenna, N. J., and O'Malley, B. W. (2002) Endocrinology 143, 2461-2465
24. de la Cruz, X., Lois, S., Sánchez-Molina, S., and Martínez-Balbás, M. A. (2005) BioEssays 27, 164-175
25. Narlikar, G. J., Fan, H. Y., and Kingston, R. E. (2002) Cell 108, 475-487
26. Li, B., Carey, M., and Workman, J. L. (2007) Cell 128, 707-719
27. Lund, A. H., and van Lohuizen, M. (2004) Curr. Opin. Cell Biol. 16, 239-246
28. Boyer, L. A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L. A., Lee, T. I., Levine, S. S., Wernig, M., Tajonar, A., Ray, M. K., Bell, G. W., Otte, A. P., Vidal, M., Gifford, D. K., Young, R. A., and Jaenisch, R. (2006) Nature 441, 349-353
29. Bracken, A. P., Dietrich, N., Pasini, D., Hansen, K. H., and Helin, K. (2006) Genes Dev. 20, 1123-1136
30. Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R. S., and Zhang, Y. (2002) Science 298, 1039-1043
31. Sparmann, A., and van Lohuizen, M. (2006) Nat. Rev. Cancer 6, 846-856
32. Schwartz, Y. B., and Pirrotta, V. (2007) Nat. Rev. Genet 8, 9-22
33. Gillespie, R. F., and Gudas, L. J. (2007) J. Mol. Biol. 372, 298-316
34. Gillespie, R. F., and Gudas, L. J. (2007) J. Biol. Chem. 282, 33421-33434
35. Keller, G. (2005) Genes Dev. 19, 1129-1155
36. Kashyap, V., Rezende, N. C., Scotland, K. B., Shaffer, S. M., Persson, J. L., Gudas, L. J., and Mongan, N. P. (2009) Stem Cells Dev. 18, 1093-1108
37. Gan, Q., Yoshida, T., McDonald, O. G., and Owens, G. K. (2007) Stem Cells 25, 2-9
38. Kimura, H., Tada, M., Nakatsuji, N., and Tada, T. (2004) Mol. Cell. Biol. 24, 5710-5720
39. Szutorisz, H., Canzonetta, C., Georgiou, A., Chow, C. M., Tora, L., and Dillon, N. (2005) Mol. Cell. Biol. 25, 1804-1820
40. Loudig, O., Babichuk, C., White, J., Abu-Abed, S., Mueller, C., and Petkovich, M. (2000) Mol. Endocrinol. 14, 1483-1497
41. Loudig, O., Maclean, G. A., Dore, N. L., Luu, L., and Petkovich, M. (2005) Biochem. J. 392, 241-248
42. LaRosa, G. J., and Gudas, L. J. (1988) Mol. Cell. Biol. 8, 3906-3917
43. Schroder, E. W., Rapaport, E., Kabcenell, A. K., and Black, P. H. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 1549-1552
44. Means, A. L., and Gudas, L. J. (1996) Cell Growth Differ. 7, 989-996
45. Hörlein, A. J., Näär, A. M., Heinzel, T., Torchia, J., Gloss, B., Kurokawa, R., Ryan, A., Kamei, Y., Söderström, M., and Glass, C. K. (1995) Nature 377, 397-404
46. Langston, A. W., Thompson, J. R., and Gudas, L. J. (1997) J. Biol. Chem. 272, 2167-2175
47. Pavri, R., Lewis, B., Kim, T. K., Dilworth, F. J., Erdjument-Bromage, H., Tempst, P., de Murcia, G., Evans, R., Chambon, P., and Reinberg, D. (2005) Mol. Cell 18, 83-96
48. Lefebvre, B., Brand, C., Lefebvre, P., and Ozato, K. (2002) Mol. Cell. Biol. 22, 1446-1459
49. Kouzarides, T. (2007) Cell 128, 693-705
50. Fischle, W., Wang, Y., and Allis, C. D. (2003) Curr. Opin. Cell Biol. 15, 172-183
51. Kirmizis, A., Bartley, S. M., Kuzmichev, A., Margueron, R., Reinberg, D., Green, R., and Farnham, P. J. (2004) Genes Dev. 18, 1592-1605
52. Cao, R., and Zhang, Y. (2004) Curr. Opin. Genet. Dev. 14, 155-164
53. Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R. M., Chevalier, B., Johnstone, S. E., Cole, M. F., Isono, K., Koseki, H., Fuchikami, T., Abe, K., Murray, H. L., Zucker, J. P., Yuan, B., Bell, G. W., Herbolsheimer, E., Hannett, N. M., Sun, K., Odom, D. T., Otte, A. P., Volkert, T. L., Bartel, D. P., Melton, D. A., Gifford, D. K., Jaenisch, R., and Young, R. A. (2006) Cell 125, 301-313
54. Newell-Price, J., Clark, A. J., and King, P. (2000) Trends Endocrinol. Metab. 11, 142-148
55. Farthing, C. R., Ficz, G., Ng, R. K., Chan, C. F., Andrews, S., Dean, W., Hemberger, M., and Reik, W. (2008) PLoS Genet. 4, e1000116
56. Deb-Rinker, P., Ly, D., Jezierski, A., Sikorska, M., and Walker, P. R. (2005) J. Biol. Chem. 280, 6257-6260
57. Delacroix, L., Moutier, E., Altobelli, G., Legras, S., Poch, O., Choukrallah, M. A., Bertin, I., Jost, B., and Davidson, I. (2010) Mol. Cell. Biol. 30, 231-244
58. Xu, L., Glass, C. K., and Rosenfeld, M. G. (1999) Curr. Opin. Genet. Dev. 9, 140-147
59. Hu, X., and Lazar, M. A. (2000) Trends Endocrinol Metab. 11, 6-10
60. Flajollet, S., Lefebvre, B., Cudejko, C., Staels, B., and Lefebvre, P. (2007) Mol. Cell. Endocrinol. 270, 23-32
61. Bird, A. (2002) Genes Dev. 16, 6-21
62. Gardiner-Garden, M., and Frommer, M. (1987) J. Mol. Biol. 196, 261-282
63. Larsen, F., Gundersen, G., Lopez, R., and Prydz, H. (1992) Genomics 13, 1095-1107
64. Jaenisch, R., and Bird, A. (2003) Nat. Genet. 33, 245-254
65. Razin, A., and Cedar, H. (1994) Cell 77, 473-476
66. Baylin, S. B., and Herman, J. G. (2000) Trends Genet. 16, 168-174
67. Herman, J. G., and Baylin, S. B. (2000) Curr. Top Microbiol. Immunol. 249, 35-54
68. Bovenzi, V., Lê, N. L., Côte, S., Sinnett, D., Momparler, L. F., and Momparler, R. L. (1999) Anticancer Drugs 10, 471-476
69. Jerónimo, C., Henrique, R., Hoque, M. O., Ribeiro, F. R., Oliveira, J., Fonseca, D., Teixeira, M. R., Lopes, C., and Sidransky, D. (2004) Clin Cancer Res. 10, 4010-4014
70. Ivanova, T., Petrenko, A., Gritsko, T., Vinokourova, S., Eshilev, E., Kobzeva, V., Kisseljov, F., and Kisseljova, N. (2002) BMC Cancer 2, 4
71. Monk, M., Boubelik, M., and Lehnert, S. (1987) Development 99, 371-382
72. Li, E. (2002) Nat. Rev. Genet. 3, 662-673
73. Futscher, B. W., Oshiro, M. M., Wozniak, R. J., Holtan, N., Hanigan, C. L., Duan, H., and Domann, F. E. (2002) Nat. Genet. 31, 175-179
74. Fouse, S. D., Shen, Y., Pellegrini, M., Cole, S., Meissner, A., Van Neste, L., Jaenisch, R., and Fan, G. (2008) Cell Stem Cell. 2, 160-169
75. Li, J. Y., Pu, M. T., Hirasawa, R., Li, B. Z., Huang, Y. N., Zeng, R., Jing, N. H., Chen, T., Li, E., Sasaki, H., and Xu, G. L. (2007) Mol. Cell. Biol. 27, 8748-8759
76. Cho, J. H., Kimura, H., Minami, T., Ohgane, J., Hattori, N., Tanaka, S., and Shiota, K. (2001) Endocrinology 142, 3389-3396
77. Missaghian, E., Kempná, P., Dick, B., Hirsch, A., Alikhani-Koupaei, R., Jégou, B., Mullis, P. E., Frey, B. M., and Flück, C. E. (2009) J. Endocrinol. 202, 99-109
78. Yin, H., and Blanchard, K. L. (2000) Blood 95, 111-119
79. Nan, X., Ng, H. H., Johnson, C. A., Laherty, C. D., Turner, B. M., Eisenman, R. N., and Bird, A. (1998) Nature 393, 386-389
80. Ng, H. H., Zhang, Y., Hendrich, B., Johnson, C. A., Turner, B. M., Erdjument-Bromage, H., Tempst, P., Reinberg, D., and Bird, A. (1999) Nat. Genet. 23, 58-61
81. Jones, P. L., Veenstra, G. J., Wade, P. A., Vermaak, D., Kass, S. U., Landsberger, N., Strouboulis, J., and Wolffe, A. P. (1998) Nat. Genet. 19, 187-191
82. Feldman, N., Gerson, A., Fang, J., Li, E., Zhang, Y., Shinkai, Y., Cedar, H., and Bergman, Y. (2006) Nat. Cell Biol. 8, 188-194
83. Pan, G., Tian, S., Nie, J., Yang, C., Ruotti, V., Wei, H., Jonsdottir, G. A., Stewart, R., and Thomson, J. A. (2007) Cell Stem. Cell 1, 299-312
84. Abu-Abed, S., Dollé, P., Metzger, D., Beckett, B., Chambon, P., and Petkovich, M. (2001) Genes Dev. 15, 226-240
85. Martinez-Ceballos, E., Chambon, P., and Gudas, L. J. (2005) J. Biol. Chem. 280, 16484-16498
86. Chisaka, O., Musci, T. S., and Capecchi, M. R. (1992) Nature 355, 516-520
87. Lufkin, T., Dierich, A., LeMeur, M., Mark, M., and Chambon, P. (1991) Cell 66, 1105-1119
88. Thompson, J. R., Chen, S. W., Ho, L., Langston, A. W., and Gudas, L. J. (1998) Dev. Dyn. 211, 97-108