Constructing transcriptional regulatory networks

Genes and Development

Volumn 19, Issue 13, 2005, Pages 1499-1511

  Blais, Alexandre ^a   Dynlacht, Brian David ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bioinformatics; ChIP on chip; Expression profiling; Transcriptional regulatory networks

Indexed keywords

RNA;

CELL; CELL CYCLE; CELL DIFFERENTIATION; CELL GROWTH; CHROMATIN; GENE CONSTRUCT; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE INTERACTION; GROWTH INHIBITION; IMMUNOPRECIPITATION; KNOCKOUT GENE; MAMMAL CELL; MOLECULAR BIOLOGY; MUSCLE DEVELOPMENT; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; RNA INTERFERENCE; TECHNIQUE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; YEAST;

ANIMALS; GENE EXPRESSION REGULATION; HUMANS; TRANSCRIPTION, GENETIC;

MAMMALIA;

EID: 22344449669     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1325605     Document Type: Review

References (76)

1. Alfarano, C., Andrade, C.E., Anthony, K., Bahroos, N., Bajec, M., Bantoft, K., Betel, D., Bobechko, B., Boutilier, K., Burgess, E., et al. 2005. The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res. 33: D418-D424.
2. Banerjee, N. and Zhang, M.Q. 2002. Functional genomics as applied to mapping transcription regulatory networks. Curr. Opin. Microbiol. 5: 313-317.
3. Bar-Joseph, Z., Gerber, G.K., Lee, T.I., Rinaldi, N.J., Yoo, J.Y., Robert, F., Gordon, D.B., Fraenkel, E., Jaakkola, T.S., Young, R.A., et al. 2003. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 21: 1337-1342.
4. Barabasi, A.L. and Oltvai, Z.N. 2004. Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5: 101-113.
5. Baum, B. and Craig, G. 2004. RNAi in a postmodern, postgenomic era. Oncogene 23: 8336-8339.
6. Beer, M.A. and Tavazoie, S. 2004. Predicting gene expression from sequence. Cell 117: 185-198.
7. Bergmann, S., Ihmels, J., and Barkai, N. 2004. Similarities and differences in genome-wide expression data of six organisms. PLoS Biol. 2: E9.
8. Bergstrom, D.A., Penn, B.H., Strand, A., Perry, R.L., Rudnicki, M.A., and Tapscott, S.J. 2002. Promoter-specific regulation of MyoD binding and signal transduction cooperate to pattern gene expression. Mol. Cell 9: 587-600.
9. Bianchi-Frias, D., Orian, A., Delrow, J.J., Vazquez, J., Rosales-Nieves, A.E., and Parkhurst, S.M. 2004. Hairy transcriptional repression targets and cofactor recruitment in Drosophila. PLoS Biol. 2: E178.
10. Blais, A. and Dynlacht, B.D. 2004. Hitting their targets: An emerging picture of E2F and cell cycle control. Curr. Opin. Genet. Dev. 14: 527-532.
11. Blais, A., Tsikitis, M., Acosta-Alvear, D., Sharan, R., Kluger, Y., and Dynlacht, B.D. 2005. An initial blueprint for myogenic differentiation. Genes & Dev. 19: 553-569.
12. Bracken, A.P., Ciro, M., Cocito, A., and Helin, K. 2004. E2F target genes: Unraveling the biology. Trends Biochem. Sci. 29: 409-417.
13. Buckingham, M. 2001. Skeletal muscle formation in vertebrates. Curr. Opin. Genet. Dev. 11: 440-448.
14. Cam, H. and Dynlacht, B.D. 2003. Emerging roles for E2F: Beyond the G1/S transition and DNA replication. Cancer Cell 3: 311-316.
15. Cam, H., Balciunaite, E., Blais, A., Spektor, A., Scarpulla, R.C., Young, R., Kluger, Y., and Dynlacht, B.D. 2004. A common set of gene regulatory networks links metabolism and growth inhibition. Mol. Cell 16: 399-411.
16. Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
17. Chen, J. and Sadowski, I. 2005. Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements. Proc. Natl. Acad. Sci. 102: 4813-4818.
18. Davidson, E.H., Rast, J.P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C.H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., et al. 2002. A genomic regulatory network for development. Science 295: 1669-1678.
19. Davidson, E.H., McClay, D.R., and Hood, L. 2003. Regulatory gene networks and the properties of the developmental process. Proc. Natl. Acad. Sci. 100: 1475-1480.
20. Dieterich, C., Grossmann, S., Tanzer, A., Ropcke, S., Arndt, P.F., Stadler, P.F., and Vingron, M. 2005. Comparative promoter region analysis powered by CORG. BMC Genomics 6: 24.
21. Dimova, D.K., Stevaux, O., Frolov, M.V., and Dyson, N.J. 2003. Cell cycle-dependent and cell cycle-independent control of transcription by the Drosophila E2F/RB pathway. Genes & Dev. 17: 2308-2320.
22. Elemento, O. and Tavazoie, S. 2005. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol. 6: R18.
23. Elkon, R., Linhart, C., Sharan, R., Shamir, R., and Shiloh, Y. 2003. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res. 13: 773-780.
24. Euskirchen, G., Royce, T.E., Bertone, P., Martone, R., Rinn, J.L., Nelson, F.K., Sayward, F., Luscombe, N.M., Miller, P., Gerstein, M., et al. 2004. CREB binds to multiple loci on human chromosome 22. Mol. Cell. Biol. 24: 3804-3814.
25. Fernandez, P.C., Frank, S.R., Wang, L., Schroeder, M., Liu, S., Greene, J., Cocito, A., and Amati, B. 2003. Genomic targets of the human c-Myc protein. Genes & Dev. 17: 1115-1129.
26. Friedman, A. and Perrimon, N. 2004. Genome-wide high-throughput screens in functional genomics. Curr. Opin. Genet. Dev. 14: 470-476.
27. Geisberg, J.V. and Struhl, K. 2004. Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo. Nucleic Acids Res. 32: e151.
28. Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.B., Reynolds, D.B., Yoo, J., et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
29. Holstege, F.C., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.
30. Horak, C.E., Luscombe, N.M., Qian, J., Bertone, P., Piccirrillo, S., Gerstein, M., and Snyder, M. 2002. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes & Dev. 16: 3017-3033.
31. Huang, E., Ishida, S., Pittman, J., Dressman, H., Bild, A., Kloos, M., D'Amico, M., Pestell, R.G., West, M., and Nevins, J.R. 2003. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat. Genet. 34: 226-230.
32. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y., and Barkai, N. 2002. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31: 370-377.
33. Ihmels, J., Bergmann, S., and Barkai, N. 2004. Defining transcription modules using large-scale gene expression data. Bioinformatics 20: 1993-2003.
34. Inoue, T., Wang, M., Ririe, T.O., Fernandes, J.S., and Sternberg, P.W. 2005. Transcriptional network underlying Caenorhabditis elegans vulval development. Proc. Natl. Acad. Sci.. 102: 4972-4977.
35. Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
36. Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., and Barabasi, A.L. 2000. The large-scale organization of metabolic networks. Nature 407: 651-654.
37. Jeong, H., Mason, S.P., Barabasi, A.L., and Oltvai, Z.N. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
38. Kato, M., Hata, N., Banerjee, N., Futcher, B., and Zhang, M.Q. 2004. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol. 5: R56.
39. Kel, A.E., Kel-Margoulis, O.V., Farnham, P.J., Bartley, S.M., Wingender, E., and Zhang, M.Q. 2001. Computer-assisted identification of cell cycle-related genes: New targets for E2F transcription factors. J. Mol. Biol. 309: 99-120.
40. Kim, J., Bhinge, A.A., Morgan, X.C., and Iyer, V.R. 2004. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nat. Methods 2: 47-53.
41. Koide, T., Hayata, T., and Cho, K.W. 2005. Xenopus as a model system to study transcriptional regulatory networks. Proc. Natl. Acad. Sci.. 102: 4943-4948.
42. Kondo, Y., Shen, L., Yan, P.S., Huang, T.H., and Issa, J.P. 2004. Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc. Natl. Acad. Sci. 101: 7398-7403.
43. Labhart, P., Karmakar, S., Salicru, E.M., Egan, B.S., Alexiadis, V., O'Malley, B.W., and Smith, C.L. 2005. Identification of target genes in breast cancer cells directly regulated by the SRC-3/AIB1 coactivator. Proc. Natl. Acad. Sci. 102: 1339-1344.
44. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 799-804.
45. Levine, M. and Davidson, E.H. 2005. Gene regulatory networks for development. Proc. Natl. Acad. Sci.. 102: 4936-4942.
46. Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A., and Gerstein, M. 2004. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312.
47. Maduro, M.F. and Rothman, J.H. 2002. Making worm guts: The gene regulatory network of the Caenorhabditis elegans endoderm. Dev. Biol. 246: 68-85.
48. Martone, R., Euskirchen, G., Bertone, P., Hartman, S., Royce, T.E., Luscombe, N.M., Rinn, J.L., Nelson, F.K., Miller, P., Gerstein, M., et al. 2003. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. 100: 12247-12252.
49. McKinsey, T.A., Zhang, C.L., and Olson, E.N. 2002. Signaling chromatin to make muscle. Curr. Opin. Cell. Biol. 14: 763-772.
50. Muller, H., Bracken, A.P., Vernell, R., Moroni, M.C., Christians, F., Grassilli, E., Prosperini, E., Vigo, E., Oliner, J.D., and Helin, K. 2001. E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes & Dev. 15: 267-285.
51. Nachman, I., Regev, A., and Friedman, N. 2004. Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 (Suppl. 1): I248-I256.
52. Newman, M.E.J. 2003. The structure and function of complex networks. SIAM Rev. 45: 167-256.
53. 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., et al. 2004. Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381.
54. Orian, A., van Steensel, B., Delrow, J., Bussemaker, H.J., Li, L., Sawado, T., Williams, E., Loo, L.W., Cowley, S.M., Yost, C., et al. 2003. Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes & Dev. 17: 1101-1114.
55. Pilpel, Y., Sudarsanam, P., and Church, G.M. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29: 153-159.
56. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
57. Ren, B., Cam, H., Takahashi, Y., Volkert, T., Terragni, J., Young, R.A., and Dynlacht, B.D. 2002. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes & Dev. 16: 245-256.
58. Roth, F.P., Hughes, J.D., Estep, P.W., and Church, G.M. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16: 939-945.
59. Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D., and Friedman, N. 2003. Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34: 166-176.
60. Sharan, R., Ovcharenko, I., Ben-Hur, A., and Karp, R.M. 2003. CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics 19 (Suppl. 1): i283-i291.
61. Siggia, E.D. 2005. Computational methods for transcriptional regulation. Curr. Opin. Genet. Dev. 15: 214-221.
62. Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S., et al. 2001. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106: 697-708.
63. Sinha, S., Blanchette, M., and Tompa, M. 2004. PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 5: 170.
64. Sonnichsen, B., Koski, L.B., Walsh, A., Marschall, P., Neumann, B., Brehm, M., Alleaume, A.M., Artelt, J., Bettencourt, P., Cassin, E., et al. 2005. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434: 462-469.
65. Stevaux, O. and Dyson, N.J. 2002. A revised picture of the E2F transcriptional network and RB function. Curr. Opin. Cell. Biol. 14: 684-691.
66. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., and Church, G.M. 1999. Systematic determination of genetic network architecture. Nat. Genet. 22: 281-285.
67. Tompa, M., Li, N., Bailey, T.L., Church, G.M., De Moor, B., Eskin, E., Favorov, A.V., Frith, M.C., Fu, Y., Kent, W.J., et al. 2005. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23: 137-144.
68. Tronche, F., Ringeisen, F., Blumenfeld, M., Yaniv, M., and Pontoglio, M. 1997. Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol. 266: 231-245.
69. van Steensel, B. and Henikoff, S. 2000. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 18: 424-428.
70. Viens, A., Mechold, U., Lehrmann, H., Harel-Bellan, A., and Ogryzko, V. 2004. Use of protein biotinylation in vivo for chromatin immunoprecipitation. Anal. Biochem. 325: 68-76.
71. Wang, Y., Liu, C.L., Storey, J.D., Tibshirani, R.J., Herschlag, D., and Brown, P.O. 2002. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. 99: 5860-5865.
72. Wasserman, W.W. and Fickett, J.W. 1998. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278: 167-181.
73. Weinmann, A.S., Yan, P.S., Oberley, M.J., Huang, T.H., and Farnham, P.J. 2002. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes & Dev. 16: 235-244.
74. Wells, J., Yan, P.S., Cechvala, M., Huang, T., and Farnham, P.J. 2003. Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene 22: 1445-1460.
75. Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M., and Eisenberg, D. 2002. DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303-305.
76. Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R.Y., Alon, U., and Margalit, H. 2004. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc. Natl. Acad. Sci. 101: 5934-5939.