Research Interests

Molecular evolution and function of RNA polymerase II
In recent years, comparative analyses of molecular sequences have had a dramatic impact on how biologists view the evolution of life.  At the same time there have been revolutionary advances in understanding the functions of key molecular machinery common to all living cells.  My research takes an integrated approach, investigating both the pattern of evolution that can be discerned from molecular sequences, as well as the evolutionary significance of key mechanistic differences found among diverse organisms.  The focus of this work is RNA polymerase II, the enzyme responsible for transcribing protein-encoding genes in all eukaryotic cells, the C-terminal domain (CTD) of RNAP II in particular.  Our overall goal is to understand how CTD-protein interactions have evolved over time, and what impact they have had on patterns of diversification found among major eukaryotic lineages.

I. The origin and evolution of the RNA polymerase II CTD

In complex eukaryotic organisms, transcription of protein-encoding genes must be controlled tightly to achieve and maintain developmental complexity.  The CTD is a key component of that control.  CTD-protein interactions are essential for many steps in the RNAP II transcription cycle, during both transcript initiation and processing, and apparently for coordinating many nuclear functions not directly related to transcription as well.  A clearly recognizable CTD has been found in RPB1 sequences from all animals, fungi and green plants examined to date.  Although it is likewise present in a number of unicellular and colonial protists, there are diverse groups of organisms that have either a highly modified or degenerate CTD, or are missing the region entirely. 

In an effort to understand the evolutionary distribution of the CTD, and the functional significance of differences found among eukaryotic organisms, we employ a variety of methods, ranging from phylogenetic and bioinformatic comparisons, to genetic analyses of yeast CTD mutants, to biochemical assays on mutated CTDs.  Below are some selected papers on CTD evolution and function.

Guo, Z. and Stiller, J.W. 2005. Comparative genomics and evolution of proteins associated with RNA polymerase II C-terminal domain. Molecular Biology and Evolution 22:2166-2178.

Guo, Z. and Stiller, J.W. 2004.  Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs BMC Genomics  5:69.

Stiller, J.W. and Cook, M.S. 2004. Functional unit of the RNA polymerase II C-terminal domain lies within heptapeptide pairs. Eukaryotic Cell 3:735-740.

Stiller, J.W. and Hall, B.D. 2002. Evolution of the RNA polymerase II C-terminal domain. Proceedings of the National Academy of Sciences  USA  99:6091-6096.


II. The evolution and molecular biology of red algae

One of the most interesting groups in which the CTD has not been evolutionarily conserved is the Rhodophyta.  Based on well-characterized fossils, red algae first appeared more than 1.2 billion years ago, making them the most ancient eukaryotic group to have attained multicellular complexity.  Despite their impressive age and great ecological diversity, however, no red alga has ever achieved the kind of true tissue development found in animals and green plants. We are investigating the hypothesis that this is due, at least in part, to different mechanisms for controlling RNAP II transcription in red algae; specifically, they lack the necessary level of transcriptional control conferred by CTD-protein interactions.

We are examining the importance of this key difference in RNAP II structure in red algae, and what it can tell us about their origin and relationships to other eukaryotic groups.  Below are some selected references of our past work on the origin and evolution of red algae.

Stiller, J.W. and Harrell, L. 2005.  The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny.  BMC Evolutionary Biology 5:71.

Waaland, J.R., Cheney, D. and Stiller J.W. 2004. Macroalgal candidates for genomics. Journal of Phycology  40:26-33.

Stiller J.W., Reel, D.C. and Johnson, J.C. 2003. The case for a single plastid origin revisited: convergent evolution in organellar genome content. Journal of Phycology  39:95-105.

Stiller, J.W, Riley, J and Hall, B.D. 2001. Are red algae plants? A critical evaluation of three key molecular data sets.  Journal of Molecular Evolution  52:527-539.


Selected Recent Publications

Stiller, J.W. and Coggins, T.C. 2006. Teaching molecular biological techniques in a research context. American Biology Teacher.  January: 595-601.

Stiller, J.W. and Harrell, L. 2005.  The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny.  BMC Evolutionary Biology 5:71.

Guo, Z. and Stiller, J.W. 2005. Comparative genomics and evolution of proteins associated with RNA polymerase II C-terminal domain. Molecular Biology and Evolution 22:2166-2178.

Powell, K. and Stiller, J.W. 2005. What’s Living in Your World? Building research partnerships for inquiry-based learning.  The Science Teacher.  December: 20-25.

Stiller, J.W. 2004. Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.  Genomics, Proteomics and Bioinformatics  2:69-75.

Guo, Z. and Stiller, J.W. 2004.  Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs. BMC Genomics 5:69.

Stiller, J.W. and Cook, M.S. 2004. Functional unit of the RNA polymerase II C-terminal domain lies within heptapeptide pairs. Eukaryotic Cell 3:735-740.

Waaland, J.R., Stiller J.W. and Cheney, D. 2004. Macroalgal candidates for genomics. Journal of Phycology  40:26-33.
Stiller, J.W. 2003. Weighing the evidence for a single origin of plastids. Journal of Phycology  39:1-3.

Stiller, J.W., Reel, D.C. and Johnson, J.C. 2003. The case for a single plastid origin revisited: convergent evolution in organellar genome content. Journal of Phycology  39:95-105.

Stiller, J.W. and Hall, B.D. 2002. Evolution of the RNA polymerase II C-terminal domain. Proceedings of the National Academy of Sciences  USA  99:6091-6096.