The challenge of modeling nuclear receptor regulatory networks in mammalian cells

Molecular and Cellular Endocrinology

Volumn 334, Issue 1-2, 2011, Pages 91-97

  Jagannathan, Vidhya ^a   Robinson Rechavi, Marc ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Bioinformatics; Epigenetics; Nuclear receptors; Systems biology; Transcription

Indexed keywords

CELL NUCLEUS RECEPTOR; CONSTITUTIVE ANDROSTANE RECEPTOR; ESTROGEN RECEPTOR ALPHA; HISTONE H3; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR; RETINOIC ACID RECEPTOR; RETINOID X RECEPTOR; STEROIDOGENIC FACTOR 1; THYROID HORMONE RECEPTOR; VITAMIN D RECEPTOR;

BIOINFORMATICS; CELL METABOLISM; DATA EXTRACTION; DATA MINING; DNA BINDING MOTIF; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETIC ENGINEERING; GENETIC EPIGENESIS; GENETIC MODEL; GENOME ANALYSIS; HISTONE MODIFICATION; HUMAN; INFORMATION SYSTEM; MAMMAL CELL; MATHEMATICAL COMPUTING; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN DNA BINDING; RECEPTOR BINDING; REVIEW; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TISSUE METABOLISM; TRANSCRIPTION REGULATION;

ANIMALS; CELL LINE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DIMERIZATION; EPIGENOMICS; FEMALE; GENE EXPRESSION; GENE REGULATORY NETWORKS; GENETIC VARIATION; GENOME; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MAMMALS; MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; RECEPTORS, CYTOPLASMIC AND NUCLEAR; SIGNAL TRANSDUCTION;

EID: 79951679438     PISSN: 03037207     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mce.2010.06.012     Document Type: Review

References (65)

1. Albert S., Gaudan S., Knigge H., Raetsch A., Delgado A., Huhse B., Kirsch H., Albers M., Rebholz-Schuhmann D., Koegl M. Computer-assisted generation of a protein-interaction database for nuclear receptors. Mol. Endocrinol. 2003, 17:1555-1567.
2. Amoutzias G.D., Pichler E.E., Mian N., De Graaf D., Imsiridou A., Robinson-Rechavi M., Bornberg-Bauer E., Robertson D.L., Oliver S.G. A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Syst. Biol. 2007, 1:34.
3. Barnett D.H., Sheng S., Charn T.H., Waheed A., Sly W.S., Lin C.Y., Liu E.T., Katzenellenbogen B.S. Estrogen receptor regulation of carbonic anhydrase XII through a distal enhancer in breast cancer. Cancer Res. 2008, 68:3505-3515.
4. Biddie S.C., John S., Hager G.L. Trends Endocrinol. Metab. 2010, 21:3-9.
5. Birkmeier, B., 2006. Integrating prior knowledge into the fitness function of an evolutionary algorithm for deriving gene regulatory networks (Master Thesis). University of Skövde, Sweden.
6. Bookout A.L., Jeong Y., Downes M., Yu R.T., Evans R.M., Mangelsdorf D.J. Anatomical profiling of nuclear receptor expression reveals a hierarchical transcriptional network. Cell 2006, 126:789-799.
7. Bretschneider N., Sara K., Seifert M., Reid G., Gannon F., Denger S. E2-mediated cathepsin D (CTSD) activation involves looping of distal enhancer elements. Mol. Oncol. 2008, 2:182-190.
8. Carroll J.S., Liu X.S., Brodsky A.S., Li W., Meyer C.A., Szary A.J., Eeckhoute J., Shao W., Hestermann E.V., Geistlinger T.R., Fox E.A., Silver P.A., Brown M. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 2005, 122:33-43.
9. Carroll J.S., Meyer C.A., Song J., Li W., Geistlinger T.R., Eeckhoute J., Brodsky A.S., Keeton E.K., Fertuck K.C., Hall G.F., Wangl Q., Bekiranov S., Sementchenko V., Fox E.A., Silver P.A., Gingeras T.R., Liu X.S., Brown M. Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 2006, 38:1289-1297.
10. Cheung E., Kraus W.L. Genomic analyses of hormone signaling and gene regulation. Annual Review of physiology 2010, 72:191-218.
11. Dekker J. Gene regulation in the third dimension. Science 2008, 319:1793-1794.
12. Della Gatta G., Bansal M., Ambesi-Impiombato A., Antonini D., Missero C., Di Bernardo D. Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. Genome Res. 2008, 18:939-948.
13. Deschenes J., Bourdeau V., White J.H., Mader S. Regulation of GREB1 transcription by estrogen receptor alpha through a multipartite enhancer spread over 20kb of upstream flanking sequences. J. Biol. Chem. 2007, 282:17335-17339.
14. Dufour C.R., Wilson B.J., Huss J.M., Kelly D.P., Alaynick W.A., Downes M., Evans R.M., Blanchette M., Giguere V. Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. Cell Metab. 2007, 5:345-356.
15. Escriva H., Bertrand S., Laudet V. The evolution of the nuclear receptor superfamily. Essays Biochem. 2004, 40:11-26.
16. Filkov V. Identifying Gene Regulatory Networks from Gene Expression Data 2005, CRC Press, Chapman & Hall.
17. Fullwood M.J., Liu M.H., Pan Y.F., Liu J., Xu H., Mohamed Y.B., Orlov Y.L., Velkov S., Ho A., Mei P.H., Chew E.G.Y., Huang P.Y.H., Welboren W.-J., Han Y., Ooi H.S., Ariyaratne P.N., Vega V.B., Luo Y., Tan P.Y., Choy P.Y., Wansa K.D.S.A., Zhao B., Lim K.S., Leow S.C., Yow J.S., Joseph R., Li H., Desai K.V., Thomsen J.S., Lee Y.K., Karuturi R.K.M., Herve T., Bourque G., Stunnenberg H.G., Ruan X., Cacheux-Rataboul V., Sung W.-K., Liu E.T., Wei C.-L., Cheung E., Ruan Y. An oestrogen-receptor-[agr]-bound human chromatin interactome. Nature 2009, 462:58-64.
18. Gao H., Falt S., Sandelin A., Gustafsson J.A., Dahlman-Wright K. Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver. Mol. Endocrinol. 2008, 22:10-22.
19. Garcia-Bassets I., Kwon Y.S., Telese F., Prefontaine G.G., Hutt K.R., Cheng C.S., Ju B.G., Ohgi K.A., Wang J., Escoubet-Lozach L., Rose D.W., Glass C.K., Fu X.D., Rosenfeld M.G. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 2007, 128:505-518.
20. Geier F., Timmer J., Fleck C. Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst. Biol. 2007, 1:11.
21. Glass C.K., Ogawa S. Combinatorial roles of nuclear receptors in inflammation and immunity. Nat. Rev. Immunol. 2006, 6:44-55.
22. Gofflot F., Chartoire N., Vasseur L., Heikkinen S., Dembele D., Le Merrer J., Auwerx J. Systematic gene expression mapping clusters nuclear receptors according to their function in the brain. Cell 2007, 131:405-418.
23. Hakim O., John S., Ling J.Q., Biddie S.C., Hoffman A.R., Hager G.L. Glucocorticoid receptor activation of the Ciz1-Lcn2 locus by long range interactions. J. Biol. Chem. 2009, 284:6048-6052.
24. Hampton O.A., Den Hollander P., Miller C.A., Delgado D.A., Li J., Coarfa C., Harris R.A., Richards S., Scherer S.E., Muzny D.M., Gibbs R.A., Lee A.V., Milosavljevic A. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res. 2009, 19:167-177.
25. He F., Balling R., Zeng A.P. Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives. J. Biotechnol. 2009, 144:190-203.
26. Holmes K.A., Song J.S., Liu X.S., Brown M., Carroll J.S. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. Cancer Res. 2008, 68:7380-7385.
27. Hu Q., Kwon Y.S., Nunez E., Cardamone M.D., Hutt K.R., Ohgi K.A., Garcia-Bassets I., Rose D.W., Glass C.K., Rosenfeld M.G., Fu X.D. Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:19199-19204.
28. Hurtado A., Holmes K.A., Geistlinger T.R., Hutcheson I.R., Nicholson R.I., Brown M., Jiang J., Howat W.J., Ali S., Carroll J.S. Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen. Nature 2008, 456:663-666.
29. Huttenhower C., Mutungu K.T., Indik N., Yang W., Schroeder M., Forman J.J., Troyanskaya O.G., Coller H.A. Detailing regulatory networks through large scale data integration. Bioinformatics 2009, 25:3267-3274.
30. Jelier R., Jenster G., Dorssers L.C., Wouters B.J., Hendriksen P.J., Mons B., Delwel R., Kors J.A. Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. BMC Bioinform. 2007, 8:14.
31. John S., Sabo P.J., Johnson T.A., Sung M.H., Biddie S.C., Lightman S.L., Voss T.C., Davis S.R., Meltzer P.S., Stamatoyannopoulos J.A., Hager G.L. Interaction of the glucocorticoid receptor with the chromatin landscape. Mol. Cell 2008, 29:611-624.
32. Karlebach G., Shamir R. Modelling and analysis of gene regulatory networks. Nat. Rev. Mol. Cell. Biol. 2008, 9:770-780.
33. Kim S., Yamazaki M., Zella L.A., Shevde N.K., Pike J.W. Activation of receptor activator of NF-kappaB ligand gene expression by 1,25-dihydroxyvitamin D3 is mediated through multiple long-range enhancers. Mol. Cell. Biol. 2006, 26:6469-6486.
34. Kininis M., Chen B.S., Diehl A.G., Isaacs G.D., Zhang T., Siepel A.C., Clark A.G., Kraus W.L. Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol. Cell. Biol. 2007, 27:5090-5104.
35. Kininis M., Isaacs G.D., Core L.J., Hah N., Kraus W.L. Postrecruitment regulation of RNA polymerase II directs rapid signaling responses at the promoters of estrogen target genes. Mol. Cell. Biol. 2009, 29:1123-1133.
36. Koczan D., Drynda S., Hecker M., Drynda A., Guthke R., Kekow J., Thiesen H.J. Molecular discrimination of responders and nonresponders to anti-TNF alpha therapy in rheumatoid arthritis by etanercept. Arthritis Res. Ther. 2008, 10:R50.
37. Kushner P.J., Agard D.A., Greene G.L., Scanlan T.S., Shiau A.K., Uht R.M., Webb P. Estrogen receptor pathways to AP-1. J. Steroid Biochem. Mol. Biol. 2000, 74:311-317.
38. Kwon Y.S., Garcia-Bassets I., Hutt K.R., Cheng C.S., Jin M., Liu D., Benner C., Wang D., YE Z., Bibikova M., Fan J.B., Duan L., Glass C.K., Rosenfeld M.G., Fu X.D. Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:4852-4857.
39. Laganiere J., Deblois G., Lefebvre C., Bataille A.R., Robert F., Giguere V. From the cover: location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:11651-11656.
40. Le Phillip P., Bahl A., Ungar L.H. Using prior knowledge to improve genetic network reconstruction from microarray data. In Silico Biol. 2004, 4:335-353.
41. Lefterova M.I., Zhang Y., Steger D.J., Schupp M., Schug J., Cristancho A., Feng D., Zhuo D., Stoeckert C.J., Liu X.S., Lazar M.A. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev. 2008, 22:2941-2952.
42. Li X., Rao S., Jiang W., Li C., Xiao Y., Guo Z., Zhang Q., Wang L., Du L., Li J., Li L., Zhang T., Wang Q.K. Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling. BMC Bioinform. 2006, 7:26.
43. Lin C.Y., Vega V.B., Thomsen J.S., Zhang T., Kong S.L., Xie M., Chiu K.P., Lipovich L., Barnett D.H., Stossi F., Yeo A., George J., Kuznetsov V.A., Lee Y.K., Charn T.H., Palanisamy N., Miller L.D., Cheung E., Katzenellenbogen B.S., Ruan Y., Bourque G., Wei C.L., Liu E.T. Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet. 2007, 3:e87.
44. Lupien M., Eeckhoute J., Meyer C.A., Krum S.A., Rhodes D.R., Liu X.S., Brown M. Coactivator function defines the active estrogen receptor alpha cistrome. Mol. Cell. Biol. 2009, 29:3413-3423.
45. Mangelsdorf D.J., Thummel C., Beato M., Herrlich P., Schutz G., Umesono K., Blumberg B., Kastner P., Mark M., Chambon P., Evans R.M. The nuclear receptor superfamily: the second decade. Cell 1995, 83:835-839.
46. Margolin A.A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Dalla Favera R., Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform. 2006, 1(7 Suppl.):S7.
47. Martin L.J., Tremblay J.J. Nuclear receptors in Leydig cell gene expression and function. Biol. Reprod. 2010.
48. Mobini R., Andersson B.A., Erjefalt J., Hahn-Zoric M., Langston M.A., Perkins A.D., Cardell L.O., Benson M. A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 receptor in allergic inflammation. BMC Syst. Biol. 2009, 3:19.
49. Needham C.J., Bradford J.R., Bulpitt A.J., Westhead D.R. A primer on learning in Bayesian networks for computational biology. PLoS Comput. Biol. 2007, 3:e129.
50. Nielsen R., Pedersen T.A., Hagenbeek D., Moulos P., Siersbaek R., Megens E., Denissov S., Borgesen M., Francoijs K.J., Mandrup S., Stunnenberg H.G. Genome-wide profiling of PPARgamma: RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev. 2008, 22:2953-2967.
51. Odom D.T., Zizlsperger N., Gordon D.B., Bell G.W., Rinaldi N.J., Murray H.L., Volkert T.L., Schreiber J., Rolfe P.A., Gifford D.K., Fraenkel E., Bell G.I., Young R.A. Control of pancreas and liver gene expression by HNF transcription factors. Science 2004, 303:1378-1381.
52. Ribeiro R.C., Kushner P.J., Baxter J.D. The nuclear hormone receptor gene superfamily. Annu. Rev. Med. 1995, 46:443-453.
53. Robinson-Rechavi M., Escriva Garcia H., Laudet V. The nuclear receptor superfamily. J. Cell Sci. 2003, 116:585-586.
54. Saramaki A., Diermeier S., Kellner R., Laitinen H., Vaisanen S., Carlberg C. Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1alpha,25-dihydroxyvitamin D3. J. Biol. Chem. 2009, 284:8073-8082.
55. Simonis M., Kooren J., de Laat W. An evaluation of 3C-based methods to capture DNA interactions. Nat. Methods 2007, 4:895-901.
56. So A.Y., Chaivorapol C., Bolton E.C., Li H., Yamamoto K.R. Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet. 2007, 3:e94.
57. Spieth C., Streichert F., Speer N., Zell A. Inferring regulatory systems with noisy pathway information. Proceeding of the German Conference on Bioinformatics 2005, 193-203.
58. Tuck D.P., Kluger H.M., Kluger Y. Characterizing disease states from topological properties of transcriptional regulatory networks. BMC Bioinform. 2006, 7:236.
59. Wang Q., Carroll J.S., Brown M. Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol. Cell 2005, 19:631-642.
60. van Someren E.P., Wessels L.F., Backer E., Reniders M.J. Genetic network modeling. Pharmacogenomics 2002, 3:507-525.
61. Wang Q., Li W., Liu X.S., Carroll J.S., Janne O.A., Keeton E.K., Chinnaiyan A.M., Pienta K.J., Brown M. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol. Cell 2007, 27:380-392.
62. Welboren W.J., Van Driel M.A., Janssen-Megens E.M., Van Heeringen S.J., Sweep F.C., Span P.N., Stunnenberg H.G. ChIP-seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J. 2009, 28:1418-1428.
63. Xie C.Q., Jeong Y., Fu M., Bookout A.L., Garcia-Barrio M.T., Sun T., Kim B.H., Xie Y., Root S., Zhang J., Xu R.H., Chen Y.E., Mangelsdorf D.J. Expression profiling of nuclear receptors in human and mouse embryonic stem cells. Mol. Endocrinol. 2009, 23:724-733.
64. Yuryev A., Mulyukov Z., Kotelnikova E., Maslov S., Egorov S., Nikitin A., Daraselia N., Mazo I. Automatic pathway building in biological association networks. BMC Bioinform. 2006, 7:171.
65. Zheng W., Long J., Gao Y.T., Li C., Zheng Y., Xiang Y.B., Wen W., Levy S., Deming S.L., Haines J.L., Gu K., Fai A.M.r, Cai Q., Lu W., Shu X.O. Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. Nat. Genet. 2009, 41:324-328.