Research: We are interested in understanding the mechanisms involved in the regulation of RNA transcription and pre-messenger RNA splicing in a broad biological context. The two systems we are currently pursuing are innate immunity and the role of gene regulation in brain development and function. Innate immunity: We have chosen the human interferon-ß gene to approach the question of how the mammalian transcription apparatus is directed to the appropriate set of genes in response to virus infection. We have characterized the structure and function of the IFN-b enhanceosome, which consists of the IFN-b transcriptional enhancer and associated proteins. These proteins include six transcriptional activators two transcriptional coactivators and a high mobility protein. The goal of these studies is to understand how multi-protein transcriptional enhancer complexes are assembled, and how they function to activate or repress gene transcription. We have also studied the signal transduction pathways leading to the activation of the interferon-ß gene. These studies led to the discovery that regulated proteolysis mediated by the ubiquitin-proteasome pathway plays a critical role in the activation of transcriptional activator proteins. Our current focus is on the function of the IKK-related kinase called IKKe, which plays a critical role in the activation of antiviral genes by IFN-b. Gene expression in the brain. The protocadherin gene cluster. The mammalian protocadherin gene cluster provides an interesting system for studying the complex mechanisms involved in regulating gene expression in the brain. Protocadherins are arranged in three gene clusters (a, b and g) spanning over 900 kb of DNA. A total of over 50 distinct protein isoforms are encoded in the gene cluster, and individual neurons express distinct combination of these isoforms. The generation of this combinatorial set of proteins involves stochastic promoter choice, monoallelic expression and alternative pre-mRNA splicing. We are interested in understanding the mechanisms that underlie these complex processes. We are also interested in the function of protocadherin proteins, which are expressed at synaptic junctions. We generated a large number of deletion mutants within the mouse gene cluster by homologous recombination, including the entire a and b gene clusters, regions within the g gene cluster and the entire a, b, and g gene clusters. The effects of these mutations on brain development and structure, physiology and behavior are being studied. We are also taking a biochemical approach to understand the function of protocadherins. First, we are studying the mechanisms by which protocadherin-a is proteolytically processed, and how the intracellular domain functions. Second, we have identified a number of proteins that interact with the intracellular domain, and are carrying out experiments to determine the function of these proteins.
Selected Publications: Innate Immunity: Gene Regulation and Signal Transduction Silverman, N., and Maniatis, T. (2001). NF-kB signaling pathways in mammalian and insect innate immunity. Genes Dev 15, 2321-2342. Fitzgerald KA, McWhirter SM, Faia KL, Rowe DC, Latz E, Golenbock DT, Coyle AJ, Liao SM, Maniatis T. (2003). IKKepsilon and TBK1 are essential components of the IRF3 signaling pathway. Nat Immunol. 4(5):491-6. Silverman N, Zhou R, Erlich RL, Hunter M, Bernstein E, Schneider D, Maniatis T. (2003). Immune activation of NF-kappaB and JNK requires Drosophila TAK1. J Biol Chem. 278(49):48928-34. McWhirter SM, Fitzgerald KA, Rosains J, Rowe DC, Golenbock DT, Maniatis T. (2004). IFN-regulatory factor 3-dependent gene expression is defective in Tbk1-deficient mouse embryonic fibroblasts. Proc Natl Acad Sci U S A. 101:233-8. Panne D, Maniatis T, Harrison SC.(2004).Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer. EMBO J. 23(22):4384-93. Zhou R, Silverman N, Hong M, Liao DS, Chung Y, Chen ZJ, Maniatis T. (2005) The role of ubiquitination in Drosophila innate immunity. J Biol Chem. 280(40):34048-55. Mechanisms of pre-mRNA splicing Maniatis, T., and Reed, R. (2002). An extensive network of coupling among gene expression machines. Nature 416, 499-506. Maniatis, T., and Tasic, B. (2002). Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418, 236-243. Ibrahim el C, Schaal TD, Hertel KJ, Reed R, Maniatis T. (2005). Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc Natl Acad Sci U S A. 102(14):5002-7. Takahara T, Tasic B, Maniatis T, Akanuma H, Yanagisawa S. (2005). Delay in synthesis of the 3' splice site promotes trans-splicing of the preceding 5' splice site. Mol Cell. 18(2):245-51. Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF. (2006) Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol. 2006;2:2006. Regulation of Protocadherin Gene Expression Wu, Q., and Maniatis, T. (1999). A striking organization of a large family of human neural cadherin-like cell adhesion genes. Cell 97, 779-790. Tasic, B., Nabholz, C. E., Baldwin, K. K., Kim, Y., Rueckert, E. H., Ribich, S. A., Cramer, P., Wu, Q., Axel, R., and Maniatis, T. (2002). Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing. Mol Cell 10, 21-33. Ribich, S., Tasic, B and Maniatis, T. (2006) Identification of long-range regulatory elements in the protocadherin-alpha gene cluster. Proc Natl Acad Sci U S A. 103(52):19719-24.
|
