Home Faculty and Research Faculty by Name Caroline Kane

Caroline Kane

Professor Emeritus of Biochemistry and Molecular Biology*
*And Member, Graduate Group in Microbiology

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Research Interests

Our goal is to understand how gene expression is controlled in eukaryotic cells. Specifically, we focus on the transcription elongation process. Regulation during elongation is involved in controlling the expression of a large number of genes, including protooncogenes and several infectious viruses. To understand this regulation, we are studying the molecular details of the transcribing complex during elongation as well as the biological effects brought about by regulated changes in this part of the transcription machinery.  We use two model systems:  Saccharomyces cerevisiae RNA polymerase II and hepatitis C virus RNA dependent RNA polymerase.

Current Projects

How does the cell regulate the synthesis of messenger RNA during transcript elongation? RNA polymerase II transcription units can be many thousands of nucleotides long, and efficient expression of such a gene's information requires the efficient elongation of the polymerase along these sequences. A variety of cellular and viral genes contain sequences within the transcription unit that are regulatory hotspots during transcription elongation. These genes include several cellular protooncogenes as well as the human immunodeficiency viruses. Transcription stops at these hotspots under specific cellular conditions, and efficient readthrough of these sites is necessary for production of the gene product. The cell modulates the recognition of these sites in ways that are not yet understood. To define the molecular mechanisms responsible for this regulation, we are using microarray genomic analysis to identify the cadre of gene expression changes that result from mutation or deletion of a variety of elongation factors in yeast. We then are using biochemistry and genetics to test the elongation regulation that influences those genes.

How do accessory elongation factors change the transcript elongation properties of RNA polymerase II? We have shown that a protein (TFIIS) known to stimulate elongation by RNA polymerase II can act upon purified RNA polymerase II. The yeast and human proteins have been studied using mutagenesis, coupled with in vivo and in vitro analysis, to identify interactions with other proteins as well as structure: function relationships. Genetic screens in yeast deleted for the gene encoding this protein have identified other genes associated with chromatin structure and other open reading frames whose involvement in elongation regulation is being analyzed. Currently we are focused on Taf14, a nuclear protein that is part of six protein complexes involved in transcription or chromatin regulatory changes.  The function of Taf14 in these complexes is not known, although its genetic interaction seems to be due to TFIIF, an initiation and elongation factor.  Other evidence implicates Taf14 in regulating the interface between transcription and the cell cycle. Biochemistry, genetics, and cell biology approaches are being used in this work.

Using Saccharomyces cerevisiae, we are also studying the function of subunits of RNA polymerase II during the elongation process, and the effect of post-translational modifications to thepolymerase that control elongation. Specifically, we are dissecting the function of reversible phosphorylation of RNA polymerase II itself in regulating gene expression. We have identified a phosphatase specific for RNA polymerase II and a cofactor essential for its activity in vitro. Structure: function analyses with the phosphatase as well as a variety of in vivo analyses are directed to understanding the role of phosphorylation.

An extension of our work with DNA dependent RNA polymerases has taken us to Hepatitis C virus that uses an RNA dependent RNA polymerase to replicate its genome.  Using purified proteins encoded by the hepatitis C virus genome, we are comparing the initiation and elongation properties of its polymerase with those we have characterized for RNA polymerase II. In addition to the clinical significance of our findings, this work provides a comparison between RNA polymerases that are nuclear vs. cytoplasmic, that use DNA vs. RNA for templates, and that initiate with the assistance of multiple host factors vs. initiation de novo. The structures of the polymerases are very similar. The mechanistic similarities and differences add to the biochemical and biological information re: the viral polymerase.

Selected Publications

Genetic interactions between TFIIF and TFIIS. [Fish, R. N., M. L. Ammermann, J. K. Davie, B. F. Lu, C. Pham, L. A. Howe, A. S. Ponticelli, and C. M. Kane (2006) Genetics 173, 1871-84]

Genetic interactions between an RNA polymerase II phosphatase and centromeric elements in Saccharomyces cerevisiae. [E. Pierstorff and C.M. Kane (2004) Mol Genet Genomics 27, 603-15]

Running with RNA polymerase: Eukaryotic transcript elongation. [K.M. Arndt, and C.M. Kane (2003) Trends in Genetics 19, 543-50]

In vitro studies of transcript initiation by E. coli RNA polymerase. I. RNA chain initiation, abortive initiation, and promoter escape at three bacteriophage promoters. [L.M. Hsu, N.V. Vo, C.M. Kane, and M.J. Chamberlin (2003) Biochemistry 42, 3777-3786]

In vitro studies of transcript initiation by E. coli RNA polymerase. II. Formation and characterization of two distinct classes of initial transcribing complexes. [N.V. Vo, L.M. Hsu, C.M. Kane, and M.J. Chamberlin (2003) Biochemistry 42, 3887-3797]

In vitro studies of transcript initiation by E. coli RNA polymerase. III. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape.[N.V. Vo, L.M. Hsu, C.M. Kane, and M.J. Chamberlin (2003) Biochemistry 42, 3798-3811]

Evaluating A Science Diversity Program at U.C. Berkeley: More Questions than Answers. [J.T. Matsui, R. Liu, and C.M. Kane (2003) Cell Biology Education 2, 117-121]

Intrinsic transcript cleavage in S. cerevisiae RNA polymerase II elongation complexes. [R.G. Weilbaecher, D.E. Awrey, A.M. Edwards, and C.M. Kane (2003) J. Biol. Chem. 278, 24189-24199]

Genetic interaction between TFIIS and the SWI/SNF chromatin remodeling complex. [J.K. Davie, and Caroline M. Kane (2000) Molecular and Cellular Biology 20, 5960-5973]

Structural basis for the species specific activity of TFIIS. [N.B. Shimasaki, and Caroline M. Kane (2000) J. Biol. Chem 275, 36541-36549]

Last Updated 2007-03-04