Ribosome biosynthesis is intimately linked to the rates of cell growth and proliferation. Transcription of the ribosomal DNA, mediated by RNA polymerase I (Pol I), is the first, rate- limiting step in ribosome biosynthesis. Based on its critical role in cell biology and its recent emergence as a therapeutic target, the overall goal of this project is to define the mechanisms that control Pol I activity and orchestrate early steps in ribosome biosynthesis. Eukaryotic RNA polymerases have specialized roles, and the three largest ribosomal RNAs are synthesized uniquely by Pol I. There is growing interest in developing Pol I as a therapeutic target for cancer, but to accomplish this goal, we must understand how the enzyme works and how it is regulated. This project will deploy a series of biochemical strategies to define enzymatic properties of Pol I and compare those properties to Pols II and III. The ribosomal DNA locus is densely packed with Pol I transcription elongation complexes, and the kinetics of transcription by these enzymes directly influence processing of the nascent rRNA. Transcription elongation efficiency is influenced by trans-acting transcription elongation factors, DNA template sequence, and metabolic status of the cell. To define how these complex biochemical processes are orchestrated this project will use a blend of genetic, genomic, biochemical and bioinformatic approaches to identify DNA sequences that control Pol I transcription elongation in vitro and in vivo. Many transcription factors that fine tune rRNA expression have been defined. Several of these transcription factors are known to affect Pols I and II, often exhibiting very different effects on the respective enzymes. To understand the principles by which gene expression is regulated there is a need to define the mechanism by which transcription factors function. Pol I is an excellent model enzyme for characterizing transcription factor function in detail. The overall goal of this project, and the Schneider lab as a whole, is to move the field toward mechanistic definition of ribosome biosynthesis. A detailed understanding of this process is fundamentally important to cell biology. Furthermore, there is growing interest in developing selective inhibitors of ribosome biosynthesis, with a focus on Pol I. Thus, there is a critical need for a more complete, mechanistic definition of Pol I function.

Public Health Relevance

Transcription of the ribosomal DNA by RNA polymerase I is the first, rate-limiting step in eukaryotic ribosome biosynthesis. Since ribosome biosynthesis is crucial to cell growth and has proven to be an excellent target for anti-cancer chemotherapy, defining the mechanisms that control RNA polymerase I activity is fundamentally and therapeutically important.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Adkins, Ronald
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University of Alabama Birmingham
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United States
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Clarke, Andrew M; Engel, Krysta L; Giles, Keith E et al. (2018) NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I. Proc Natl Acad Sci U S A 115:E11633-E11641
Appling, Francis D; Scull, Catherine E; Lucius, Aaron L et al. (2018) The A12.2 Subunit Is an Intrinsic Destabilizer of the RNA Polymerase I Elongation Complex. Biophys J 114:2507-2515
Wei, Ting; Najmi, Saman M; Liu, Hester et al. (2018) Small-Molecule Targeting of RNA Polymerase I Activates a Conserved Transcription Elongation Checkpoint. Cell Rep 23:404-414
Ucuncuoglu, S; Schneider, D A; Weeks, E R et al. (2017) Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics. Methods Enzymol 582:415-435
Zhang, Yinfeng; Najmi, Saman M; Schneider, David A (2017) Transcription factors that influence RNA polymerases I and II: To what extent is mechanism of action conserved? Biochim Biophys Acta Gene Regul Mech 1860:246-255
Appling, Francis D; Lucius, Aaron L; Schneider, David A (2017) Quantifying the influence of 5'-RNA modifications on RNA polymerase I activity. Biophys Chem 230:84-88
Cornelison, Robert; Dobbin, Zachary C; Katre, Ashwini A et al. (2017) Targeting RNA-Polymerase I in Both Chemosensitive and Chemoresistant Populations in Epithelial Ovarian Cancer. Clin Cancer Res 23:6529-6540
Zhang, Yinfeng; French, Sarah L; Beyer, Ann L et al. (2016) The Transcription Factor THO Promotes Transcription Initiation and Elongation by RNA Polymerase I. J Biol Chem 291:3010-8
Ucuncuoglu, Suleyman; Engel, Krysta L; Purohit, Prashant K et al. (2016) Direct Characterization of Transcription Elongation by RNA Polymerase I. PLoS One 11:e0159527
Engel, Krysta L; French, Sarah L; Viktorovskaya, Olga V et al. (2015) Spt6 Is Essential for rRNA Synthesis by RNA Polymerase I. Mol Cell Biol 35:2321-31

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