Prof. Rivka Dikstein Phone: +972-8-934-2117; Fax: +972-8-934-4118 Email: rivka.dikstein@weizmann.ac.il Molecular Mechanisms of Transcription Regulation Transcription of protein encoding genes is an intricate and highly regulated process that produces a remarkable diversity of gene expression patterns. Elucidation of the mechanisms that generate such diversity is an important challenge and the primary goal of the research in our lab. We are investigating the mechanism underlying both basal and regulated transcription. Basal Transcription Characterization of the mammalian core promoter The core promoter comprises the transcription start site and flanking sequences that anchor general transcription factors (GTFs) and RNA pol II. Until recently the core promoter was thought to be a general element common to most genes. However sequence analysis has revealed unexpected diversity among core promoters. Many promoters do not contain any known core promoter elements and the best-known element, the TATA box is found in only ~20% of human promoters. To investigate the mammalian core promoter we are combining bioinformatic tools with molecular analysis. Our findings of the past few years revealed important new features of the mammalian core promoter and provide insights into its evolution. We found unexpected links between core promoter elements (initiation) to other properties, including transcription elongation (Amir-Zilberstein et al 2007), gene size (Moshonov et al., 2008) and protein translation (Elfakess and Dikstein, 2008). Currently we extend these studies with a particular emphasis on the biochemical and molecular features of newly identified proximal promoter elements and their role in post-transcriptional stages of gene expression. TFIID Among the general transcription factors TFIID is the major core promoter binding factor. TFIID is comprised of the TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). TAFs control transcription at multiple levels and possess gene-specific as well as general functions. Although our understanding of TFIID is continuously expanding, to date our knowledge on the specific function of individual TAFs is still very limited. We are investigating the function of the TAFs by characterizing their biochemical properties, their core promoter functions, their relations with other transcription regulators and their physiological functions. Regulated Transcription NF-kB An activated transcription regulatory pathway that we are studying involves the transcription factor NF-kB. NF-kB regulates the expression of genes involved in immune responses, viral infections, cytokine signaling and stress. While the NF-kB signaling pathways have been studied in great detail, much less is known about the nuclear events that lead to activation of genes by NF-kB. Our goal is to decipher the molecular means by which NF-kB activates the transcription of its native target genes. We have previously determined how, in principle, NF-kB-regulated anti-apoptotic genes are rapidly activated in response to extra-cellular signals. Most recently we discovered that these genes are differentially controlled at the elongation step by negative elongation factors. Our current research is directed toward the mechanism by which NF-kB target genes are induced so rapidly and what role is played by transcription elongation factors. Since NF-kB is directly involved in several diseases, it is an important target for drug development. Understanding the molecular basis of transcription regulation by NF-kB may help in identifying more specific targets for drugs, which will selectively manipulate expression of NF-kB-regulated genes under disease conditions. MicroRNA transcription MicroRNAs are non-coding small RNA that silence the expression of target genes. Beside the fact that microRNAs are transcribed by Pol II very little is known about the transcription regulation of the microRNA genes. Our goal is to determine the properties of microRNA transcription by combining bioinformatics and molecular tools. Selected Publications Ainbinder, E., Amir-Zilberstein, L., Yamaguchi, Y., Handa, H. and Dikstein R. (2004). Elongation inhibition by DSIF is regulated by the A20 promoter via a novel negative element and NF-kB. Mol. Cell. Biol. 24, 2444-2454. Shao, H., Revach, M., Moshonov, S., Tzuman Y., Gazit, K., Albeck, S., Unger. T., Dikstein R. (2005). Core promoter binding by histone fold-like TAF complexes. Mol. Cell. Biol. 25, 206-219. Amir-Zilberstein, L., Ainbinder, E., Toube, L., Yamaguchi, Y. Hiroshi Handa and Dikstein, R. (2007). Differential regulation of NF-kB by elongation factors is determined by core promoter type. Mol. Cell. Biol. 27, 5246-5259. Lantner, F., Starlets, D., Gore, Y., Flaishon, L., Yamit-Hezi, A., Dikstein R., Leng, L., Bucala, R., Machluf, Y., Oren, M., Shachar I. (2007). CD74 induces TAp63 expression leading to B cell survival. Blood 110, 4303-4311. Amir-Zilberstein and Dikstein R. (2008). Interplay between E-box and NF-kB in regulation of A20 gene by DSIF. J. Biol. Chem. 283, 1317-1323. Moshonov, S., Elfakess, R., Golan-Mashiach, M., Sinvani, H. and Dikstein, R. (2008). Links between core promoter and basic gene features influence gene expression. BMC Genomics 9, 92-96. Elfakess R. and Dikstein R. (2008). A Translation Initiation Element Specific to mRNAs with Very Short 5'UTR that also Regulates Transcription. PLoS ONE. 3(8):e3094. Yarden G., Elfakess R. and Dikstein R. (2009). Characterization of sINR, a strict version of the Initiator core promoter element. Nucleic Acids Res. 37, 4234-4246. Gazit, K. Moshonov, S., Elfakess, R., Sharon, M., Mengus, G., Davidson, I. and Dikstein R. (2009). TAF4/4b-TAF12 displays a unique mode of DNA binding and is required for core promoter function of a subset of genes. J. Biol. Chem. 284, 26286-26296. Bar, N. and Dikstein, R. (2009). miR-22 forms a regulatory loop in PTEN/AKT pathway and modulates signaling kinetics. Submitted.