Genome-wide identification of post-translational modulators of transcription factor activity in human B cells (original) (raw)
Faith, J.J. et al. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol.5, e8 (2007).
Friedman, N. Inferring cellular networks using probabilistic graphical models. Science303, 799–805 (2004). ArticleCAS Google Scholar
Gardner, T.S., di Bernardo, D., Lorenz, D. & Collins, J.J. Inferring genetic networks and identifying compound mode of action via expression profiling. Science301, 102–105 (2003). ArticleCAS Google Scholar
Basso, K. et al. Reverse engineering of regulatory networks in human B cells. Nat. Genet.37, 382–390 (2005). ArticleCAS Google Scholar
Elkon, R., Linhart, C., Sharan, R., Shamir, R. & Shiloh, Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res.13, 773–780 (2003). ArticleCAS Google Scholar
Stuart, J.M., Segal, E., Koller, D. & Kim, S.K.A. Gene-coexpression network for global discovery of conserved genetic modules. Science302, 249–255 (2003). ArticleCAS Google Scholar
Zeitlinger, J. et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell113, 395–404 (2003). ArticleCAS Google Scholar
Luscombe, N.M. et al. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature431, 308–312 (2004). ArticleCAS Google Scholar
Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet.34, 166–176 (2003). ArticleCAS Google Scholar
Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science290, 2306–2309 (2000). ArticleCAS Google Scholar
Linding, R. et al. Systematic discovery of in vivo phosphorylation networks. Cell129, 1415–1426 (2007). ArticleCAS Google Scholar
Cover, T.M. & Thomas, J. Elements of Information Theory edn. 2 (Wiley Interscience, Hoboken, New Jersey, USA, 2006). Google Scholar
Basso, K. et al. Reverse engineering of regulatory networks in human B cells. Nat. Genet.37, 382–390 (2005). ArticleCAS Google Scholar
Mani, K.M. et al. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol. Syst. Biol.4, 169 (2008). Article Google Scholar
Dang, C.V. et al. The c-Myc target gene network. Semin. Cancer Biol.16, 253–264 (2006). ArticleCAS Google Scholar
Dominguez-Sola, D. et al. Non-transcriptional control of DNA replication by c-Myc. Nature448, 445–451 (2007). ArticleCAS Google Scholar
Pelengaris, S., Khan, M. & Evan, G. c-MYC: more than just a matter of life and death. Nat. Rev. Cancer2, 764–776 (2002). ArticleCAS Google Scholar
Zeller, K.I., Jegga, A.G., Aronow, B.J., O'Donnell, K.A. & Dang, C.V. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Genome Biol.4, R69 (2003).
Zeller, K.I., Jegga, A., Aronow, B., O'Donnell, K. & Dang, C. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Genome Biol.4, R69 (2003).
Patel, J.H. et al. The c-MYC oncoprotein is a substrate of the acetyltransferases hGCN5/PCAF and TIP60. Mol. Cell. Biol.24, 10826–10834 (2004). ArticleCAS Google Scholar
Sears, R. et al. Multiple Ras-dependent phosphorylation pathways regulate Myc protein stability. Genes Dev.14, 2501–2514 (2000). ArticleCAS Google Scholar
Yu, H. et al. High-quality binary protein interaction map of the yeast interactome network. Science322, 104–110 (2008). ArticleCAS Google Scholar
Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res.31, 374–378 (2003). ArticleCAS Google Scholar
Tamaskovic, R., Bichsel, S.J. & Hemmings, B.A. NDR family of AGC kinases–essential regulators of the cell cycle and morphogenesis. FEBS Lett.546, 73–80 (2003). ArticleCAS Google Scholar
Patel, J.H. & McMahon, S.B. BCL2 is a downstream effector of MIZ-1 essential for blocking c-MYC-induced apoptosis. J. Biol. Chem.282, 5–13 (2007). ArticleCAS Google Scholar
Schuhmacher, M. et al. The transcriptional program of a human B cell line in response to Myc. Nucleic Acids Res.29, 397–406 (2001). ArticleCAS Google Scholar
Wu, K.J. et al. Direct activation of TERT transcription by c-MYC. Nat. Genet.21, 220–224 (1999). ArticleCAS Google Scholar
Seoane, J., Le, H.V. & Massague, J. Myc suppression of the p21Cip1 Cdk inhibitor influences the outcome of the p53 response to DNA damage. Nature419, 729–734 (2002). ArticleCAS Google Scholar
St-Pierre, B., Flock, G., Zacksenhaus, E. & Egan, S.E. Stra13 homodimers repress transcription through class B E-box elements. J. Biol. Chem.277, 46544–46551 (2002). ArticleCAS Google Scholar
Wanzel, M., Herold, S. & Eilers, M. Transcriptional repression by Myc. Trends Cell Biol.13, 146–150 (2003). ArticleCAS Google Scholar
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA102, 15545–15550 (2005). ArticleCAS Google Scholar
Molkentin, J.D. et al. MEF2B is a potent transactivator expressed in early myogenic lineages. Mol. Cell. Biol.16, 3814–3824 (1996). ArticleCAS Google Scholar
Wade, P.A. Transcriptional control at regulatory checkpoints by histone deacetylases: molecular connections between cancer and chromatin. Hum. Mol. Genet.10, 693–698 (2001). ArticleCAS Google Scholar
Satou, A., Taira, T., Iguchi-Ariga, S.M.M. & Ariga, H. A novel transrepression pathway of c-Myc. Recruitment of a transcriptional corepressor complex to c-Myc by MM-1, a c-Myc-binding protein. J. Biol. Chem.276, 46562–46567 (2001). ArticleCAS Google Scholar
Matsuoka, Y., Fukamachi, K., Uehara, N., Tsuda, H. & Tsubura, A. Induction of a novel histone deacetylase 1/c-Myc/Mnt/Max complex formation is implicated in parity-induced refractoriness to mammary carcinogenesis. Cancer Sci.99, 309–315 (2008). ArticleCAS Google Scholar
Margolin, A.A. et al. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc. Natl. Acad. Sci. USA106, 244–249 (2009). ArticleCAS Google Scholar
Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods4, 651–657 (2007). ArticleCAS Google Scholar
Steffen, M., Petti, A. & Aach, J., D'haeseleer, P. & Church, G. Automated modelling of signal transduction networks. BMC Bioinformatics3, 34 (2002). Article Google Scholar
Hopkins, A.L. & Groom, C.R. The druggable genome. Nat. Rev. Drug Discov.1, 727–730 (2002). ArticleCAS Google Scholar
Margolin, A. et al. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics7, S7 (2006).
Niiro, H. & Clark, E.A. Regulation of B-cell fate by antigen-receptor signals. Nat. Rev. Immunol.2, 945–956 (2002). ArticleCAS Google Scholar
Storey, J.D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA100, 9440–9445 (2003). ArticleCAS Google Scholar
Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res.31, 51–54 (2003). ArticleCAS Google Scholar
Bereshchenko, O.R., Gu, W. & Dalla-Favera, R. Acetylation inactivates the transcriptional repressor BCL6. Nat. Genet.32, 606–613 (2002). ArticleCAS Google Scholar
Chang, C.C., Ye, B.H., Chaganti, R.S. & Dalla-Favera, R. BCL-6, a POZ/zinc-finger protein, is a sequence-specific transcriptional repressor. Proc. Natl. Acad. Sci. USA93, 6947–6952 (1996). ArticleCAS Google Scholar
Phan, R.T., Saito, M., Basso, K., Niu, H. & Dalla-Favera, R. BCL6 interacts with the transcription factor Miz-1 to suppress the cyclin-dependent kinase inhibitor p21 and cell cycle arrest in germinal center B cells. Nat. Immunol.6, 1054–1060 (2005). ArticleCAS Google Scholar
Niu, H., Cattoretti, G. & Dalla-Favera, R. BCL6 controls the expression of the B7–1/CD80 costimulatory receptor in germinal center B cells. J. Exp. Med.198, 211–221 (2003). ArticleCAS Google Scholar
Pasqualucci, L. et al. Mutations of the BCL6 proto-oncogene disrupt its negative autoregulation in diffuse large B-cell lymphoma. Blood101, 2914–2923 (2003). ArticleCAS Google Scholar
Lois, C., Hong, E.J., Pease, S., Brown, E.J. & Baltimore, D. Germline transmission and tissue-specific expression of transgenes delivered by lentiviral vectors. Science295, 868–872 (2002). ArticleCAS Google Scholar
Naldini, L. et al. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science272, 263–267 (1996). ArticleCAS Google Scholar