Transcription in eukaryotes requires RNA polymerase II (Pol II) to faithfully synthesize RNA relative to DNA sequence. Pol II must also successfully negotiate obstacles within chromatin templates and coordinate cotranscriptional events. Disruption of any of these processes may alter gene expression outcomes and derange cellular growth or physiology. Pol II, like all multisubunit cellular RNA polymerases (msRNAPs), contains an essential active site domain ? the trigger loop (TL) ? that participates in all basic nucleotide addition cycle (NAC) functions. Changes to Pol II catalytic activity have the power to alter every phase of transcription: initiation, elongation, termination, and cotranscriptional RNA processing. It is therefore likely that evolution of Pol II function has involved complex trade-offs between the rate, efficiency and fidelity of these processes. Structural, biochemical and genetic studies alike on Pol II from Saccharomyces cerevisiae have enabled critical insight into eukaryotic transcription. The high conservation of the S. cerevisiae transcription machinery and its amenability to a wide-range of experimental approaches make yeast uniquely suited to decipher gene expression mechanisms. We leverage novel approaches from high-throughput quantitative phenotyping, structural analysis of unique Pol II variants, and determination of Pol II-natural product interactions to test existing, and generate new, models for Pol II function. Misregulation of gene expression is a major contributor to human disease. Basic research into transcription mechanisms enables the defects in transcription found in disease states to be better understood.
This project aims to use molecular, genetic, biochemical, genomic, and computational studies to reveal transcription mechanisms in eukaryotes at the most fundamental level. Transcription is a critical event for gene expression. The model organism we use is the budding yeast Saccharomyces cerevisiae. The RNA polymerase enzymes that control gene expression in this model organism are highly related to those in humans and can have similar or identical functions. Many diseases are caused by alterations in gene expression and understanding how RNA polymerases work and are regulated will impact our understanding of gene expression in humans.
|Malik, Indranil; Qiu, Chenxi; Snavely, Thomas et al. (2017) Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo. Nucleic Acids Res 45:4431-4451|
|Qiu, Chenxi; Erinne, Olivia C; Dave, Jui M et al. (2016) High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLoS Genet 12:e1006321|
|Bird, Jeremy G; Zhang, Yu; Tian, Yuan et al. (2016) The mechanism of RNA 5? capping with NAD+, NADH and desphospho-CoA. Nature 535:444-7|
|Kaster, Benjamin C; Knippa, Kevin C; Kaplan, Craig D et al. (2016) RNA Polymerase II Trigger Loop Mobility: INDIRECT EFFECTS OF Rpb9. J Biol Chem 291:14883-95|
|Cui, Ping; Jin, Huiyan; Vutukuru, Manjula Ramya et al. (2016) Relationships Between RNA Polymerase II Activity and Spt Elongation Factors to Spt- Phenotype and Growth in Saccharomyces cerevisiae. G3 (Bethesda) 6:2489-504|
|Barnes, Christopher O; Calero, Monica; Malik, Indranil et al. (2015) Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Mol Cell 59:258-69|
|Murakami, Kenji; Mattei, Pierre-Jean; Davis, Ralph E et al. (2015) Uncoupling Promoter Opening from Start-Site Scanning. Mol Cell 59:133-8|
|Jeronimo, Célia; Watanabe, Shinya; Kaplan, Craig D et al. (2015) The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Mol Cell 58:1113-23|
|Cabart, Pavel; Jin, Huiyan; Li, Liangtao et al. (2014) Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis. Transcription 5:|
|Jin, Huiyan; Kaplan, Craig D (2014) Relationships of RNA polymerase II genetic interactors to transcription start site usage defects and growth in Saccharomyces cerevisiae. G3 (Bethesda) 5:21-33|
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