Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  O'Geen, Henriette ^a   Lin, Yu Hsuan ^b   Xu, Xiaoqin ^a   Echipare, Lorigail ^a   Komashko, Vitalina M ^a   He, Daniel ^a   Frietze, Seth ^a   Tanabe, Osamu ^b   Shi, Lihong ^b   Sartor, Maureen A ^b   Engel, James D ^b   Farnham, Peggy J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEAR RECEPTOR NR2C2; RNA; TRANSCRIPTION FACTOR ELK 4; TRANSCRIPTION FACTOR ETS; NR2C2 PROTEIN, HUMAN; STEROID RECEPTOR; THYROID HORMONE RECEPTOR;

ARTICLE; BINDING SITE; BIOINFORMATICS; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; CELL METABOLISM; CELL STRAIN HEPG2; CELL STRAIN K 562; CELL TYPE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; GENE IDENTIFICATION; GENE TARGETING; GENOME ANALYSIS; HELA CELL; HIGH THROUGHPUT SCREENING; HISTONE MODIFICATION; HUMAN; HUMAN CELL; IN VIVO STUDY; NUCLEOTIDE SEQUENCE; PREDICTION; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; RECEPTOR BINDING; RNA METABOLISM; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETICS; HUMAN GENOME; METABOLISM; MOLECULAR GENETICS; NUCLEOSOME; POLYMERASE CHAIN REACTION; REGULATORY SEQUENCE; REPRODUCIBILITY; TUMOR CELL LINE;

BASE SEQUENCE; BINDING SITES; BIOLOGICAL PROCESSES; CELL LINE, TUMOR; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; POLYMERASE CHAIN REACTION; PROTEIN BINDING; PROTO-ONCOGENE PROTEINS C-ETS; RECEPTORS, STEROID; RECEPTORS, THYROID HORMONE; REGULATORY SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS;

EID: 78649545910     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-689     Document Type: Article

References (42)

1. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Reviews Genetics 2009, 10:252-263.
2. Farnham PJ. Insights from genomic profiling of transcription factors. Nature Rev Genet 2009, 605-616. 10.1038/nrg2636, 2846386, 19668247.
3. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nature Rev Genet 2009, 669-680. 10.1038/nrg2641, 19736561.
4. Mangelsdorf DJ, Thummel C, Beato M, Herrlich P, Schutz G, Umesono K, Blumberg B, Kastner P, Mark M, Chambon P, Evans RM. The nuclear receptor superfamily: the second decade. Cell 1995, 83:835-839. 10.1016/0092-8674(95)90199-X, 8521507.
5. Sandelin A, Wasserman WW. Prediction of nuclear hormone receptor response elements. Mol Endocrinol 2005, 19:595-606. 10.1210/me.2004-0101, 15563547.
6. Noy N. Ligand specificity of nuclear hormone receptors: sifting through promiscuity. Biochemistry 2007, 46:13461-13467. 10.1021/bi7018699, 17983246.
7. Lee YF, Lee HJ, Chang C. Recent advances in the TR2 and TR4 orphan receptors of the nuclear receptor superfamily. J Steroid Biochem Mol Biol 2002, 81:291-308. 10.1016/S0960-0760(02)00118-8, 12361719.
8. Su Liu SX, Lee Y, Chang C. Physiological Functions of TR2 and TR4 Orphan Nuclear Receptor. 2010, 327-343. Nuclear Receptors: Current Concepts and Future Challenges: Springer Netherlands.
9. Chang C, Da Silva SL, Ideta R, Lee Y, Yeh S, Burbach JP. Human and rat TR4 orphan receptors specify a subclass of the steroid receptor superfamily. Proc Natl Acad Sci USA 1994, 91:6040-6044. 10.1073/pnas.91.13.6040, 44133, 8016112.
10. Bookout AL, Jeong Y, Downes M, Yu RT, Evans RM, Mangelsdorf DJ. Anatomical profiling of nuclear receptor expression reveals a hierarchical transcriptional network. Cell 2006, 126:789-799. 10.1016/j.cell.2006.06.049, 16923397.
11. Lee YF, Pan HJ, Burbach JP, Morkin E, Chang C. Identification of direct repeat 4 as a positive regulatory element for the human TR4 orphan receptor. A modulator for the thyroid hormone target genes. J Biol Chem 1997, 272:12215-12220. 10.1074/jbc.272.18.12215, 9115296.
12. Tanabe O, Shen Y, Liu Q, Campbell AD, Kuroha T, Yamamoto M, Engel JD. The TR2 and TR4 orphan nuclear receptors repress Gata1 transcription. Genes Dev 2007, 21:2832-2844. 10.1101/gad.1593307, 2045135, 17974920.
13. Tanabe O, Katsuoka F, Campbell AD, Song W, Yamamoto M, Tanimoto K, Engel JD. An embryonic/fetal beta-type globin gene repressor contains a nuclear receptor TR2/TR4 heterodimer. EMBO J 2002, 21:3434-3442. 10.1093/emboj/cdf340, 126089, 12093744.
14. Omori A, Tanabe O, Engel JD, Fukamizu A, Tanimoto K. Adult stage gamma-globin silencing is mediated by a promoter direct repeat element. Mol Cell Biol 2005, 25:3443-3451. 10.1128/MCB.25.9.3443-3451.2005, 1084292, 15831451.
15. Tanabe O, McPhee D, Kobayashi S, Shen Y, Brandt W, Jiang X, Campbell AD, Chen YT, Chang C, Yamamoto M, Tanimoto K, Engel JD. Embryonic and fetal beta-globin gene repression by the orphan nuclear receptors, TR2 and TR4. EMBO J 2007, 26:2295-2306. 10.1038/sj.emboj.7601676, 1864974, 17431400.
16. Liu NC, Lin WJ, Kim E, Collins LL, Lin HY, Yu IC, Sparks JD, Chen LM, Lee YF, Chang C. Loss of TR4 orphan nuclear receptor reduces phosphoenolpyruvate carboxykinase-mediated gluconeogenesis. Diabetes 2007, 56:2901-2909. 10.2337/db07-0359, 17827404.
17. Kim E, Yang Z, Liu NC, Chang C. Induction of apolipoprotein E expression by TR4 orphan nuclear receptor via 5' proximal promoter region. Biochem Biophys Res Commun 2005, 328:85-90. 10.1016/j.bbrc.2004.12.146, 15670754.
18. Chen LM, Wang RS, Lee YF, Liu NC, Chang YJ, Wu CC, Xie S, Hung YC, Chang C. Subfertility with defective folliculogenesis in female mice lacking testicular orphan nuclear receptor 4. Mol Endocrinol 2008, 22:858-867. 10.1210/me.2007-0181, 2725750, 18174360.
19. Shyr CR, Kang HY, Tsai MY, Liu NC, Ku PY, Huang KE, Chang C. Roles of testicular orphan nuclear receptors 2 and 4 in early embryonic development and embryonic stem cells. Endocrinology 2009, 150:2454-2462. 10.1210/en.2008-1165, 19131575.
20. Xie S, Lee YF, Kim E, Chen LM, Ni J, Fang LY, Liu S, Lin SJ, Abe J, Berk B, Ho FM, Chang C. TR4 nuclear receptor functions as a fatty acid sensor to modulate CD36 expression and foam cell formation. Proc Natl Acad Sci USA 2009, 106:13353-13358. 10.1073/pnas.0905724106, 2726407, 19666541.
21. Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludaescher B, Korf I, Farnham PJ. Sole-search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res 2010, 38:e13. 10.1093/nar/gkp1012, 2817454, 19906703.
22. Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals iterchangeable roles of E2F family members. Genome Res 2007, 17:1550-1561. 10.1101/gr.6783507, 2045138, 17908821.
23. Fry CJ, Pearson A, Malinowski E, Bartley SM, Greenblatt J, Farnham PJ. Activation of the murine dihydrofolate reductase promoter by E2F1: A requirement for CBP recruitment. J Biol Chem 1999, 274:15883-15891. 10.1074/jbc.274.22.15883, 10336493.
24. Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell 2009, 36:667-681. 10.1016/j.molcel.2009.11.001, 2784893, 19941826.
25. Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics 26:456-463. 10.1093/bioinformatics/btp683, 20007254.
26. Tsai NP, Huq M, Gupta P, Yamamoto K, Kagechika H, Wei LN. Activation of testicular orphan receptor 4 by fatty acids. Biochim Biophys Acta 2009, 1789:734-740. 2784022, 19800043.
27. Lee CH, Chinpaisal C, Wei LN. A novel nuclear receptor heterodimerization pathway mediated by orphan receptors TR2 and TR4. J Biol Chem 1998, 273:25209-25215. 10.1074/jbc.273.39.25209, 9737983.
28. Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 2010, 140:744-752. 10.1016/j.cell.2010.01.044, 20211142.
29. White R, Morganstein D, Christian M, Seth A, Herzog B, Parker MG. Role of RIP140 in metabolic tissues: connections to disease. FEBS Lett 2008, 582:39-45. 10.1016/j.febslet.2007.11.017, 18023280.
30. Huq MD, Gupta P, Tsai NP, Wei LN. Modulation of testicular receptor 4 activity by mitogen-activated protein kinase-mediated phosphorylation. Mol Cell Proteomics 2006, 5:2072-2082. 10.1074/mcp.M600180-MCP200, 16887930.
31. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 2007, 39:1235-1244. 10.1038/ng2117, 17873876.
32. Lee YF, Young WJ, Burbach JP, Chang C. Negative feedback control of the retinoid-retinoic acid/retinoid X receptor pathway by the human TR4 orphan receptor, a member of the steroid receptor superfamily. J Biol Chem 1998, 273:13437-13443. 10.1074/jbc.273.22.13437, 9593676.
33. Jin V, Rabinvich A, Squazzo SL, Green R, Farnham PJ. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data-a case study using E2F1. Genome Research 2006, 16:1585-1595. 10.1101/gr.5520206, 1665642, 17053090.
34. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C. Clustering of DNA sequences in human promoters. Genome Res 2004, 14:1562-1574. 10.1101/gr.1953904, 509265, 15256515.
35. Jin V, Apostolos J, Nagisetty NS, Farnham PJ. W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data. Bioinformatics 2009, 25:3191-3193. 10.1093/bioinformatics/btp570, 2778340, 19797408.
36. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-seq data. Nature Methods 2008, 5:829-834. 10.1038/nmeth.1246, 2917543, 19160518.
37. Boros J, Donaldson IJ, O'Donnell A, Odrowaz ZA, Zeef L, Lupien M, Meyer CA, Liu XS, Brown M, Sharrocks AD. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res 2009, 19:1963-1973. 10.1101/gr.093047.109, 2775591, 19687146.
38. Boros J, O'Donnell A, Donaldson IJ, Kasza A, Zeef L, Sharrocks AD. Overlapping promoter targeting by Elk-1 and other divergent ETS-domain transcription factor family members. Nucleic Acids Res 2009, 37:7368-7380. 10.1093/nar/gkp804, 2794171, 19789270.
39. O'Donnell A, Yang SH, Sharrocks AD. MAP kinase-mediated c-fos regulation relies on a histone acetylation relay switch. Mol Cell 2008, 29:780-785.
40. Gomez-Valades AG, Vidal-Alabro A, Molas M, Boada J, Bermudez J, Bartrons R, Perales JC. Overcoming diabetes-induced hyperglycemia through inhibition of hepatic phosphoenolpyruvate carboxykinase (GTP) with RNAi. Mol Ther 2006, 13:401-410. 10.1016/j.ymthe.2005.08.026, 16271515.
41. Valera A, Pujol A, Pelegrin M, Bosch F. Transgenic mice overexpressing phosphoenolpyruvate carboxykinase develop non-insulin-dependent diabetes mellitus. Proc Natl Acad Sci USA 1994, 91:9151-9154. 10.1073/pnas.91.19.9151, 44765, 8090784.
42. O'Geen H, Frietze S, Farnham PJ. Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol Biol 2010, 649:437-455.