Department of Biochemistry
School of Medicine & Biomedical Sciences
Faculty
ALFRED PONTICELLI, Ph.D.
Associate Professor
email: asp@buffalo.edu
Molecular Mechanisms of Eukaryotic RNA Polymerase II Transcription
The synthesis of messenger RNA from protein-encoding (class II) genes in eukaryotic organisms is a regulated multi-stage process that involves the concerted action of RNA polymerase II (RNAPII) and a host of auxiliary factors. A subset of these required accessory factors are known as the general transcription factors (GTFs) that includes transcription factor IIA (TFIIA), TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. Some of the main objectives in the study of RNAPII transcription are to determine the structures and functions of the GTFs and other auxiliary proteins, to define the network of molecular interactions between them, and to determine the precise molecular mechanisms underlying each stage of the transcription cycle.
In our laboratory we are using combined genetic, molecular biological and biochemical approaches to elucidate molecular mechanisms of RNAPII transcription in both the yeast Saccharomyces cerevisiae and in human cells. Using a combination of site-directed mutagenesis, in vivo phenotypic analyses, in vitro transcription and both protein-nucleic acid and protein-protein interaction studies, we are currently investigating the concerted mechanistic roles played by TFIIB, TFIIF, and the RNAPII active center during the stages of transcription initiation, promoter clearance and elongation.
Selected Recent Publications
Dermody J.L., Dreyfuss J.M., Villén J., Ogundipe B., Gygi S.P., Park, P.J., Ponticelli, A.S., Moore, C.L., Buratowski, S. and Buchelli, M.E. (2008). Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation. PLoS ONE 3: e3273.
Khaperskyy, D.A., Ammerman, M.L., Majovski, R.C. and Ponticelli, A.S. (2008). Functions of Saccharomyces cerevisiae TFIIF during transcription start site utilization. Mol. Cell. Biol. 28: 3757-3766.
Fish, R.N., Ammerman, M.L., Davie, J.K., Lu, B.F., Pham, C., Howe, L., Ponticelli, A.S. and Kane, C.M. (2006). Genetic interactions between TFIIF and TFIIS. Genetics 173: 1871-1884Majovski, R.C., Khaperskyy, D.A., Ghazy, M.A. and Ponticelli, A.S. (2005). A functional role for the switch 2 region of yeast RNAPII in transcription start site utilization and abortive initiation. J. Biol. Chem. 280: 34917-34923
Pal, M., Ponticelli, A.S. and Luse, D.S. (2005). The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II. Molecular Cell 19: 101-110.
Ghazy, M.A., Brodie, S.A., Ammerman, M.L., Ziegler, L.M. and Ponticelli, A.S. (2004). Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II. Mol. Cell. Biol. 24: 10975-10985.
Ziegler, L.M., Khaperskyy, D.A., Ammerman, M.L. and Ponticelli, A.S. (2003). Yeast RNA polymerase II lacking the Rpb9 subunit is impaired for interaction with transcription factor IIF. J. Biol. Chem. 278: 48950-48956.
Pardee, T.S., Ghazy, M.A. and Ponticelli, A.S. (2003). Yeast and human RNA polymerase II elongation complexes: Evidence for functional differences and post-initiation recruitment of factors. Euk. Cell 2: 318-327.
Faitar, S.L., Brodie, S.A. and Ponticelli, A.S. (2001). Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites. Mol. Cell. Biol. 21: 4427-4440.
Bangur, C.S., Faitar, S.L., Folster, J.P. and Ponticelli, A.S. (1999) An interaction between the N-terminal region and the core domain of yeast TFIIB promotes the formation of TATA-binding protein-TFIIB-DNA complexes. J. Biol. Chem. 274: 23203-23209.
Pardee, T.S., Bangur, C.S. and Ponticelli, A.S. (1998) The N-terminal region of yeast TFIIB contains two adjacent functional domains involved in stable RNA polymerase II binding and transcription start site selection. J. Biol. Chem. 273: 17859-17864.
Bangur, C.S., Pardee, T.S. and Ponticelli, A.S. (1997) Mutational analysis of the D1/E1 core helices and the conserved N-terminal region of yeast transcription factor IIB (TFIIB): Identification of an N-terminal mutant that stabilizes TATA-binding protein-TFIIB-DNA complexes. Mol. Cell. Biol. 17: 6784-6793.