Area of Interest
Research in my laboratory is aimed at deciphering basic mechanisms of gene expression as governed by DNA binding proteins and chromatin structure. We use the yeast Saccharomyces cerevisiae as a model system, as it is a simple eukaryote that can be easily manipulated both genetically and biochemically in the laboratory. Many basic molecular and biochemical mechanisms elucidated in yeast have been extrapolated to other eukaryotes.
Current research in my laboratory focuses on what we refer to as “extra-transcriptional functions” of the RNA Polymerase III system in eukaryotes. RNA polymerase III (Pol III) is one of three eukaryotic transcription complexes, and was identified as the enzyme responsible for synthesis of transfer RNA and a limited number of other small RNAs. Pol III transcription at tRNA genes (tDNAs) requires the binding of two transcription factor complexes, TFIIIC and TFIIIB, which then recruit the Pol III enzymatic transcription machinery to form large and stable macromolecular complexes on chromosomes.
Earlier work in my lab demonstrated that Pol III complexes assembled at tDNAs act as heterochromatin barriers, as the tDNA adjacent to the repressed HMR mating locus in yeast also functions to prevent the spreading of chromatin mediated gene silencing. We also have shown that tDNAs can act as chromatin insulators, in that they can also function to block activation of RNA Polymerase II (Pol II) transcription when placed between a promoter and transcription factor binding sites.
In addition to acting as chromatin boundaries as described above, evidence is accumulating that points to a larger role for the Pol III transcription system in various other nuclear processes, including effects on nucleosome positioning, global genome organization, and other effects on RNA polymerase II transcription. Recently, we have found that TFIIIC can directly bind to and regulate transcription from an RNA polymerase II promoter. This appears to be the first demonstration of a Pol III factor directly regulating a Pol II transcribed gene, and suggests a more general extra-transcriptional role for TFIIIC in sculpting genome architecture and function.
Our most recent work has shown yet another extra-transcriptional function for tDNAs, as they can block the progression of cryptic intergenic Pol II transcription. Many recent studies have demonstrated the existence of pervasive genome-wide Pol II transcription, and we have shown that if such transcription is not terminated (by an intervening tDNA or otherwise), deleterious transcriptional interference of neighboring genes can occur. Our current work is continuing to assess the genome-wide extra-transcriptional impacts of the Pol III complex in yeast.
Transcription factor Reb1 is required for proper transcriptional start site selection
at the divergently transcribed TFC6-ESC2 locus in Saccharomyces cerevisiae.
Qing Wang and David Donze
Gene, Vol. 594, 108-116 (2016)
Compromised RNA Polymerase III complex assembly leads to local alterations of intergenic
RNA Polymerase II transcription in Saccharomyces cerevisiae.
Qing Wang, Asawari Korde, Chance M. Nowak, Dong-Ha Oh, Maheshi Dassanayake, and David Donze
BMC Biology, 12:89 doi:10.1186/s12915-014-0089-x (2014)
Intergenic Transcriptional Interference Is Blocked by RNA Polymerase III Transcription
Factor TFIIIB in Saccharomyces cerevisiae.
Asawari Korde, Jessica M. Rosselot, and David Donze
Genetics, Vol. 196, 427-438 (2014)
TFIIIC Localises Budding Yeast ETC Sites to the Nuclear Periphery.
Shin-ichiro Hiraga, Sotirios Botsios, David Donze and Anne D. Donaldson
Molecular Biology of the Cell, Vol. 23, 2741-54 (2012)
Extra-transcriptional functions of RNA Polymerase III complexes: TFIIIC as a potential global chromatin bookmark.
Gene, Vol. 493, 169-75 (2012)
Autoregulation of an RNA polymerase II promoter by the RNA polymerase III transcription factor III C (TFIIIC) complex.
Richard A. Kleinschmidt, Kimberly E. LeBlanc, and David Donze
Proc. Nat. Acad. Sci. USA, Vol. 108, 8385-8389 (2011)
TFIIIC binding sites function as both heterochromatin barriers and chromatin insulators in S. cerevisiae.
Tiffany A. Simms, Sandra L. Dugas, Jason C. Gremillion, Megan E. Ibos, M. Nicole Dandurand, Tasha T. Toliver, Daniel J. Edwards, and David Donze
Eukaryotic Cell, Vol. 7, 2078-2086 (2008)
Requirement of Nhp6 proteins for transcription of a subset of tDNAs and heterochromatin barrier function in Saccharomyces cerevisiae.
Priscilla Braglia, Sandra L. Dugas, David Donze and Giorgio Dieci
Molecular and Cellular Biology, Vol. 27, 1545-1557 (2007)