Complexity of the RAR‐mediated transcriptional regulatory programs

Sub-Cellular Biochemistry

Volumn 70, Issue , 2014, Pages 203-225

  Liu, Zhijie ^a   Hu, Qidong ^a,b   Rosenfeld, Michael G ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR; ISOPROTEIN; LIGAND; LONG UNTRANSLATED RNA; RETINOIC ACID RECEPTOR; RETINOID X RECEPTOR;

CHEMISTRY; CHROMATIN; DNA RESPONSIVE ELEMENT; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE; REVIEW; SIGNAL TRANSDUCTION;

CHROMATIN; GENE EXPRESSION REGULATION; HUMANS; LIGANDS; PROTEIN BINDING; PROTEIN ISOFORMS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, ESTROGEN; RECEPTORS, RETINOIC ACID; RESPONSE ELEMENTS; RETINOID X RECEPTORS; RNA, LONG NONCODING; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 84910141042     PISSN: 03060225     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-94-017-9050-5_10     Document Type: Article

References (118)

1. Belikov S, Holmqvist PH, Astrand C, Wrange O (2012) FoxA1 and glucocorticoid receptor crosstalk via histone H4K16 acetylation at a hormone regulated enhancer. Exp Cell Res 318:61-74
2. Benkoussa M, Brand C, Delmotte MH, Formstecher P, Lefebvre P (2002) Retinoic acid receptors inhibit AP1 activation by regulating extracellular signal-regulated kinase and CBP recruitment to an AP1-responsive promoter. Mol Cell Biol 22:4522-4534
3. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE et al (2007) Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project. Nature 447:799-816
4. Blanco JC, Minucci S, Lu J, Yang XJ, Walker KK, Chen H, Evans RM, Nakatani Y, Ozato K (1998) The histone acetylase PCAF is a nuclear receptor coactivator. Genes Dev 12:1638-1651
5. Brown K, Chen Y, Underhill TM, Mymryk JS, Torchia J (2003) The coactivator p/CIP/SRC-3 facilitates retinoic acid receptor signaling via recruitment of GCN5. J Biol Chem 278:39402-39412
6. Chakravarti D, LaMorte VJ, Nelson MC, Nakajima T, Schulman IG, Juguilon H, Montminy M, Evans RM (1996) Role of CBP/P300 in nuclear receptor signalling. Nature 383:99-103
7. Chambon P (1996) A decade of molecular biology of retinoic acid receptors. Faseb J 10:940-954
8. Chen D, Ma H, Hong H, Koh SS, Huang SM, Schurter BT, Aswad DW, Stallcup MR (1999) Regulation of transcription by a protein methyltransferase. Science 284:2174-2177
9. Chen JD, Evans RM (1995) A transcriptional co-repressor that interacts with nuclear hormone receptors. Nature 377:454-457
10. Chen JY, Penco S, Ostrowski J, Balaguer P, Pons M, Starrett JE, Reczek P, Chambon P, Gronemeyer H (1995) RAR-specific agonist/antagonists which dissociate transactivation and AP1 transrepression inhibit anchorage-independent cell proliferation. EMBO J 14:1187-1197
11. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G et al (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149-1154
12. Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K (2012) Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res 22:490-503
13. Cho YS, Kim EJ, Park UH, Sin HS, Um SJ (2006) Additional sex comb-like 1 (ASXL1), in cooperation with SRC-1, acts as a ligand-dependent coactivator for retinoic acid receptor. J Biol Chem 281:17588-17598
14. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44:667-678
15. Colley SM, Leedman PJ (2011) Steroid receptor RNA activator-A nuclear receptor coregulator with multiple partners: insights and challenges. Biochimie 93:1966-1972
16. Cooper C, Vincett D, Yan Y, Hamedani MK, Myal Y, Leygue E (2011) Steroid receptor RNA activator bi-faceted genetic system: heads or tails? Biochimie 93:1973-1980
17. Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL (2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell 50:212-222
18. De Carvalho DD, Binato R, Pereira WO, Leroy JM, Colassanti MD, Proto-Siqueira R, Bueno-Da-Silva AE, Zago MA, Zanichelli MA, Abdelhay E et al (2011) BCR-ABLmediated upregulation of PRAME is responsible for knocking down TRAIL in CML patients. Oncogene 30:223-233
19. de The H, Vivanco-Ruiz MM, Tiollais P, Stunnenberg H, Dejean A (1990) Identification of a retinoic acid responsive element in the retinoic acid receptor beta gene. Nature 343:177-180
20. Dedieu S, Lefebvre P (2006) Retinoids interfere with the AP1 signalling pathway in human breast cancer cells. Cell Signal 18:889-898
21. Delacroix L, Moutier E, Altobelli G, Legras S, Poch O, Choukrallah MA, Bertin I, Jost B, Davidson I (2010) Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic fibroblasts and embryonic stem cells. Mol Cell Biol 30:231-244
22. Dilworth FJ, Fromental-Ramain C, Yamamoto K, Chambon P (2000) ATP-driven chromatin remodeling activity and histone acetyltransferases act sequentially during transactivation by RAR/RXR In vitro. Mol Cell 6:1049-1058
23. DiSepio D, Sutter M, Johnson AT, Chandraratna RA, Nagpal S (1999) Identification of the AP1- antagonism domain of retinoic acid receptors. Mol Cell Biol Res Commun: MCBRC 1:7-13
24. Durand B, Saunders M, Leroy P, Leid M, Chambon P (1992) All-trans and 9-cis retinoic acid induction of CRABPII transcription is mediated by RAR-RXR heterodimers bound to DR1 and DR2 repeated motifs. Cell 71:73-85
25. Easwaran V, Pishvaian M, Salimuddin, Byers S (1999) Cross-regulation of beta-catenin- LEF/TCF and retinoid signaling pathways. Curr Biol 9:1415-1418
26. Epping MT, Wang L, Edel MJ, Carlee L, Hernandez M, Bernards R (2005) The human tumor antigen PRAME is a dominant repressor of retinoic acid receptor signaling. Cell 122:835-847
27. Epping MT, Wang L, Plumb JA, Lieb M, Gronemeyer H, Brown R, Bernards R (2007) A functional genetic screen identifies retinoic acid signaling as a target of histone deacetylase inhibitors. Proc Natl Acad Sci USA 104:17777-17782
28. Fanjul A, Dawson MI, Hobbs PD, Jong L, Cameron JF, Harlev E, Graupner G, Lu XP, Pfahl M (1994) A new class of retinoids with selective inhibition of AP-1 inhibits proliferation. Nature 372:107-111
29. Fernandes I, Bastien Y, Wai T, Nygard K, Lin R, Cormier O, Lee HS, Eng F, Bertos NR, Pelletier N et al (2003) Ligand-dependent nuclear receptor corepressor LCoR functions by histone deacetylase-dependent and -independent mechanisms. Mol Cell 11:139-150
30. Franco PJ, Li G, Wei LN (2003) Interaction of nuclear receptor zinc finger DNA binding domains with histone deacetylase. Mol Cell Endocrinol 206:1-12
31. Fujiki R, Chikanishi T, Hashiba W, Ito H, Takada I, Roeder RG, Kitagawa H, Kato S (2009) GlcNAcylation of a histone methyltransferase in retinoic-acid-induced granulopoiesis. Nature 459:455-459
32. Ghisletti S, Huang W, Ogawa S, Pascual G, Lin ME, Willson TM, Rosenfeld MG, Glass CK (2007) Parallel SUMOylation-dependent pathways mediate gene- and signal-specific transrepression by LXRs and PPARgamma. Mol Cell 25:57-70
33. Gianni M, Bauer A, Garattini E, Chambon P, Rochette-Egly C (2002) Phosphorylation by p38MAPK and recruitment of SUG-1 are required for RA-induced RAR gamma degradation and transactivation. EMBO J 21:3760-3769
34. Glass CK, Rosenfeld MG (2000) The coregulator exchange in transcriptional functions of nuclear receptors. Genes Dev 14:121-141
35. Gurevich I, Aneskievich BJ (2009) Liganded RARalpha and RARgamma interact with but are repressed by TNIP1. Biochem Biophys Res Commun 389:409-414
36. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227
37. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L et al (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477:295-300
38. Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145:622-634
39. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW et al (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459:108-112
40. Heintzman ND, Ren B (2009) Finding distal regulatory elements in the human genome. Curr Opin Genet Dev 19:541-549
41. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311-318
42. Hermanson O, Glass CK, Rosenfeld MG (2002) Nuclear receptor coregulators: multiple modes of modification. Trends Endocrinol Metab 13:55-60
43. Hong SH, David G, Wong CW, Dejean A, Privalsky ML (1997) SMRT corepressor interacts with PLZF and with the PML-retinoic acid receptor alpha (RARalpha) and PLZFRARalpha oncoproteins associated with acute promyelocytic leukemia. Proc Natl Acad Sci USA 94:9028-9033
44. Horlein AJ, Naar AM, Heinzel T, Torchia J, Gloss B, Kurokawa R, Ryan A, Kamei Y, Soderstrom M, Glass CK et al (1995) Ligand-independent repression by the thyroid hormone receptor mediated by a nuclear receptor co-repressor. Nature 377:397-404
45. Hou Z, Peng H, White DE, Negorev DG, Maul GG, Feng Y, Longmore GD, Waxman S, Zelent A, Rauscher FJ 3rd (2010) LIM protein Ajuba functions as a nuclear receptor corepressor and negatively regulates retinoic acid signaling. Proc Natl Acad Sci USA 107:2938-2943
46. Hu Q, Tanasa B, Trabucchi M, Li W, Zhang J, Ohgi KA, Rose DW, Glass CK, Rosenfeld MG (2012) DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. Nat Struct Mol Biol
47. Hu X, Chen Y, Farooqui M, Thomas MC, Chiang CM, Wei LN (2004) Suppressive effect of receptor-interacting protein 140 on coregulator binding to retinoic acid receptor complexes, histone-modifying enzyme activity, and gene activation. J Biol Chem 279:319-325
48. Hua S, Kittler R, White KP (2009) Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell 137:1259-1271
49. Huq MD, Ha SG, Wei LN (2008) Modulation of retinoic acid receptor alpha activity by lysine methylation in the DNA binding domain. J Proteome Res 7:4538-4545
50. Huq MD, Tsai NP, Khan SA, Wei LN (2007) Lysine trimethylation of retinoic acid receptoralpha: a novel means to regulate receptor function. Mol Cell Proteomics: MCP 6:677-688
51. Kashyap V, Gudas LJ (2010) Epigenetic regulatory mechanisms distinguish retinoic acid-mediated transcriptional responses in stem cells and fibroblasts. J Biol Chem 285:14534-14548
52. Khetchoumian K, Teletin M, Tisserand J, Mark M, Herquel B, Ignat M, Zucman-Rossi J, Cammas F, Lerouge T, Thibault C et al (2007) Loss of Trim24 (Tif1alpha) gene function confers oncogenic activity to retinoic acid receptor alpha. Nat Genet 39:1500-1506
53. Kim JH, Lee JM, Nam HJ, Choi HJ, Yang JW, Lee JS, Kim MH, Kim SI, Chung CH, Kim KI et al (2007) SUMOylation of pontin chromatin-remodeling complex reveals a signal integration code in prostate cancer cells. Proc Natl Acad Sci USA 104:20793-20798
54. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S et al (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465:182-187
55. Lafyatis R, Kim SJ, Angel P, Roberts AB, Sporn MB, Karin M, Wilder RL (1990) Interleukin-1 stimulates and all-trans-retinoic acid inhibits collagenase gene expression through its 5' activator protein-1-binding site. Mol Endocrinol 4:973-980
56. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494:497-501
57. Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M et al (2013) Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498:511-515
58. Langlais D, Couture C, Balsalobre A, Drouin J (2012) The Stat3/GR interaction code: predictive value of direct/indirect DNA recruitment for transcription outcome. Mol Cell 47:38-49
59. Laperriere D, Wang TT, White JH, Mader S (2007) Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genom 8:23
60. Le May N, Iltis I, Ame JC, Zhovmer A, Biard D, Egly JM, Schreiber V, Coin F (2012) Poly (ADP-ribose) glycohydrolase regulates retinoic acid receptor-mediated gene expression. Mol Cell 48:785-798
61. Le May N, Fradin D, Iltis I, Bougneres P, Egly JM (2012) XPG and XPF endonucleases trigger chromatin looping and DNA demethylation for accurate expression of activated genes. Mol Cell 47:622-632
62. Le May N, Mota-Fernandes D, Velez-Cruz R, Iltis I, Biard D, Egly JM (2010) NER factors are recruited to active promoters and facilitate chromatin modification for transcription in the absence of exogenous genotoxic attack. Mol Cell 38:54-66
63. Lee HK, Park UH, Kim EJ, Um SJ (2007) MED25 is distinct from TRAP220/MED1 in cooperating with CBP for retinoid receptor activation. EMBO J 26:3545-3557
64. Lee S, Lee DK, Dou Y, Lee J, Lee B, Kwak E, Kong YY, Lee SK, Roeder RG, Lee JW (2006) Coactivator as a target gene specificity determinant for histone H3 lysine 4 methyltransferases. Proc Natl Acad Sci USA 103:15392-15397
65. Lee SW, Cho YS, Na JM, Park UH, Kang M, Kim EJ, Um SJ (2010) ASXL1 represses retinoic acid receptor-mediated transcription through associating with HP1 and LSD1. J Biol Chem 285:18-29
66. Leygue E (2007) Steroid receptor RNA activator (SRA1): unusual bifaceted gene products with suspected relevance to breast cancer. Nucl Receptor Signal 5:e006
67. Li HJ, Haque ZK, Chen A, Mendelsohn M (2007) RIF-1, a novel nuclear receptor corepressor that associates with the nuclear matrix. J Cell Biochem 102:1021-1035
68. Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X et al (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498:516-520
69. Lin F, Xiao D, Kolluri SK, Zhang X (2000) Unique anti-activator protein-1 activity of retinoic acid receptor beta. Cancer Res 60:3271-3280
70. Lindahl T, Wood RD (1999) Quality control by DNA repair. Science 286:1897-1905
71. Liu W, Ma Q, Wong K, Li W, Ohgi K, Zhang J, Aggarwal AK, Rosenfeld MG (2013) Brd4 and JMJD6-associated anti-pause enhancers in regulation of transcriptional pause release. Cell 155:1581-1595
72. Loudig O, Babichuk C, White J, Abu-Abed S, Mueller C, Petkovich M (2000) Cytochrome P450RAI(CYP26) promoter: a distinct composite retinoic acid response element underlies the complex regulation of retinoic acid metabolism. Mol Endocrinol 14:1483-1497
73. Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK (2011) Liganddependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol 12:R2
74. Mangelsdorf DJ, Evans RM (1995) The RXR heterodimers and orphan receptors. Cell 83:841-850
75. Mangelsdorf DJ, Thummel C, Beato M, Herrlich P, Schutz G, Umesono K, Blumberg B, Kastner P, Mark M, Chambon P et al (1995) The nuclear receptor superfamily: the second decade. Cell 83:835-839
76. Mangelsdorf DJ, Umesono K, Kliewer SA, Borgmeyer U, Ong ES, Evans RM (1991) A direct repeat in the cellular retinol-binding protein type II gene confers differential regulation by RXR and RAR. Cell 66:555-561
77. Mengus G, May M, Carre L, Chambon P, Davidson I (1997) Human TAF(II)135 potentiates transcriptional activation by the AF-2s of the retinoic acid, vitamin D3, and thyroid hormone receptors in mammalian cells. Genes Dev 11:1381-1395
78. Moon M, Um SJ, Kim EJ (2012) CAC1 negatively regulates RARalpha activity through cooperation with HDAC. Biochem Biophys Res Commun 427:41-46
79. Nagy L, Kao HY, Chakravarti D, Lin RJ, Hassig CA, Ayer DE, Schreiber SL, Evans RM (1997) Nuclear receptor repression mediated by a complex containing SMRT, mSin3A, and histone deacetylase. Cell 89:373-380
80. Nicholson RC, Mader S, Nagpal S, Leid M, Rochette-Egly C, Chambon P (1990) Negative regulation of the rat stromelysin gene promoter by retinoic acid is mediated by an AP1 binding site. EMBO J 9:4443-4454
81. Nouspikel T (2009) DNA repair in mammalian cells: nucleotide excision repair: variations on versatility. Cell Mol Life Sci: CMLS 66:994-1009
82. Onate SA, Tsai SY, Tsai MJ, O'Malley BW (1995) Sequence and characterization of a coactivator for the steroid hormone receptor superfamily. Science 270:1354-1357
83. Pascual G, Fong AL, Ogawa S, Gamliel A, Li AC, Perissi V, Rose DW, Willson TM, Rosenfeld MG, Glass CK (2005) A SUMOylation-dependent pathway mediates transrepression of inflammatory response genes by PPAR-gamma. Nature 437:759-763
84. Pascual G, Sullivan AL, Ogawa S, Gamliel A, Perissi V, Rosenfeld MG, Glass CK (2007) Anti-inflammatory and antidiabetic roles of PPARgamma. Novartis Found Symp 286:183- 196; discussion 196-203
85. Passeron T, Valencia JC, Namiki T, Vieira WD, Passeron H, Miyamura Y, Hearing VJ (2009) Upregulation of SOX9 inhibits the growth of human and mouse melanomas and restores their sensitivity to retinoic acid. J Clin Invest 119:954-963
86. Perissi V, Aggarwal A, Glass CK, Rose DW, Rosenfeld MG (2004) A corepressor/coactivator exchange complex required for transcriptional activation by nuclear receptors and other regulated transcription factors. Cell 116:511-526
87. Perissi V, Jepsen K, Glass CK, Rosenfeld MG (2010) Deconstructing repression: evolving models of co-repressor action. Nat Rev Genet 11:109-123
88. Perissi V, Rosenfeld MG (2005) Controlling nuclear receptors: the circular logic of cofactor cycles. Nat Rev Mol Cell Biol 6:542-554
89. Perissi V, Scafoglio C, Zhang J, Ohgi KA, Rose DW, Glass CK, Rosenfeld MG (2008) TBL1 and TBLR1 phosphorylation on regulated gene promoters overcomes dual CtBP and NCoR/SMRT transcriptional repression checkpoints. Mol Cell 29:755-766
90. Polak P, Domany E (2006) Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genom 7:133
91. Qiu J, Shi G, Jia Y, Li J, Wu M, Dong S, Wong J (2010) The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation. Cell Res 20:908-918
92. Resche-Rigon M, Gronemeyer H (1998) Therapeutic potential of selective modulators of nuclear receptor action. Curr Opin Chem Biol 2:501-507
93. Rochette-Egly C, Plassat JL, Taneja R, Chambon P (2000) The AF-1 and AF-2 activating domains of retinoic acid receptor-alpha (RARalpha) and their phosphorylation are differentially involved in parietal endodermal differentiation of F9 cells and retinoid-induced expression of target genes. Mol Endocrinol 14:1398-1410
94. Rosenfeld MG, Lunyak VV, Glass CK (2006) Sensors and signals: a coactivator/corepressor/ epigenetic code for integrating signal-dependent programs of transcriptional response. Genes Dev 20:1405-1428
95. Ross-Innes CS, Stark R, Holmes KA, Schmidt D, Spyrou C, Russell R, Massie CE, Vowler SL, Eldridge M, Carroll JS (2010) Cooperative interaction between retinoic acid receptoralpha and estrogen receptor in breast cancer. Genes Dev 24:171-182
96. Schule R, Rangarajan P, Yang N, Kliewer S, Ransone LJ, Bolado J, Verma IM, Evans RM (1991) Retinoic acid is a negative regulator of AP-1-responsive genes. Proc Natl Acad Sci USA 88:6092-6096
97. Schule R, Umesono K, Mangelsdorf DJ, Bolado J, Pike JW, Evans RM (1990) Jun-Fos and receptors for vitamins A and D recognize a common response element in the human osteocalcin gene. Cell 61:497-504
98. Shao W, Halachmi S, Brown M (2002) ERAP140, a conserved tissue-specific nuclear receptor coactivator. Mol Cell Biol 22:3358-3372
99. Shao W, Rosenauer A, Mann K, Chang CP, Rachez C, Freedman LP, Miller WH Jr (2000) Ligand-inducible interaction of the DRIP/TRAP coactivator complex with retinoid receptors in retinoic acid-sensitive and-resistant acute promyelocytic leukemia cells. Blood 96:2233-2239
100. Surjit M, Ganti KP, Mukherji A, Ye T, Hua G, Metzger D, Li M, Chambon P (2011) Widespread negative response elements mediate direct repression by agonist-liganded glucocorticoid receptor. Cell 145:224-241
101. Si J, Mueller L, Collins SJ (2007) CaMKII regulates retinoic acid receptor transcriptional activity and the differentiation of myeloid leukemia cells. J Clin Invest 117:1412-1421
102. Smith WC, Nakshatri H, Leroy P, Rees J, Chambon P (1991) A retinoic acid response element is present in the mouse cellular retinol binding protein I (mCRBPI) promoter. EMBO J 10:2223-2230
103. Suzukawa K, Colburn NH (2002) AP-1 transrepressing retinoic acid does not deplete coactivators or AP-1 monomers but may target specific Jun or Fos containing dimers. Oncogene 21:2181-2190
104. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329:689-693
105. Torchia J, Rose DW, Inostroza J, Kamei Y, Westin S, Glass CK, Rosenfeld MG (1997) The transcriptional co-activator p/CIP binds CBP and mediates nuclear-receptor function. Nature 387:677-684
106. Venteclef N, Jakobsson T, Ehrlund A, Damdimopoulos A, Mikkonen L, Ellis E, Nilsson LM, Parini P, Janne OA, Gustafsson JA et al (2010) GPS2-dependent corepressor/SUMO pathways govern anti-inflammatory actions of LRH-1 and LXRbeta in the hepatic acute phase response. Genes Dev 24:381-395
107. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854-858
108. Voegel JJ, Heine MJ, Zechel C, Chambon P, Gronemeyer H (1996) TIF2, a 160 kDa transcriptional mediator for the ligand-dependent activation function AF-2 of nuclear receptors. EMBO J 15:3667-3675
109. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA et al (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474:390-394
110. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA et al (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120-124
111. Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138:1019-1031
112. Yang-Yen HF, Zhang XK, Graupner G, Tzukerman M, Sakamoto B, Karin M, Pfahl M (1991) Antagonism between retinoic acid receptors and AP-1: implications for tumor promotion and inflammation. New Biol 3:1206-1219
113. Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD, Dorrestein PC, Rosenfeld MG (2011) ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147:773-788
114. Yang Q, Sakurai T, Kakudo K (2002) Retinoid, retinoic acid receptor beta and breast cancer. Breast Cancer Res Treat 76:167-173
115. Zhang XK, Liu Y, Lee MO (1996) Retinoid receptors in human lung cancer and breast cancer. Mutat Res 350:267-277
116. Zhao X, Patton JR, Davis SL, Florence B, Ames SJ, Spanjaard RA (2004) Regulation of nuclear receptor activity by a pseudouridine synthase through posttranscriptional modification of steroid receptor RNA activator. Mol Cell 15:549-558
117. Zhao X, Patton JR, Ghosh SK, Fischel-Ghodsian N, Shen L, Spanjaard RA (2007) Pus3pand Pus1p-dependent pseudouridylation of steroid receptor RNA activator controls a functional switch that regulates nuclear receptor signaling. Mol Endocrinol 21:686-699
118. Zhou XF, Shen XQ, Shemshedini L (1999) Ligand-activated retinoic acid receptor inhibits AP-1 transactivation by disrupting c-Jun/c-Fos dimerization. Mol Endocrinol 13:276-285