Transcription elongation and termination by RNA polymerase II are complex processes that determine the fate of the primary transcript thereby regulate gene expression. A picture is emerging in which there is more than one mode of transcription termination. This has been best examined in the yeast Saccharomyces cerevisiae. In the two conditions, different sets of proteins are involved depending upon RNA sequence signals and the primary transcript's length. In one striking example, conditional transcription termination of a non-coding RNA upstream of the IMD2 gene regulates the expression of IMP dehydrogenase, IMD2's protein product. RNA polymerase II's selection of an initiation site and TFIIB, are implicated in this process. The goal of this project is to elucidate the details of this regulatory strategy and to dissect the requirements by which RNA polymerase II chooses a termination mechanism. IMD2 serves as a useful model to understand and unravel the different mechanisms of termination. Regulation of this gene by nucleotides is seen in organisms from yeast to humans and IMP dehydrogenase is a biomedically important enzyme. Mutations in human IMPDH are linked to retinitis pigmentosa. Small molecules that inhibit it are effective drugs in wide use as valuable immunosuppressants in organ transplant recipients. This proposal will investigate the basic mechanisms of transcription initiation and termination by RNA polymerase II that allow guanine regulation of yeast IMD2. This includes the sliding search for initiation sites by pol II, the interaction of initiator and terminator regions of chromatin, the coupling of termination to exosome degradation of non-coding RNAs, and the activity of the putative helicase Sen1 in yeast and Setx in humans. The human ortholog of SEN1, SETX, is of biomedical importance since its dysfunction results in the neurodegenerative diseases Ataxia and Ocular Apraxia (AOA) type 2 and Amyotrophic Lateral Sclerosis (ALS) type 4. Unraveling this protein's biochemical and biological function will be important for understanding the pathophysiological basis of these diseases.

Public Health Relevance

Project Narrative The cellular machinery that decodes (transcribes) genetic information is complex and its failure to function properly leads to a number of human diseases. This project uses a model organism in which genes, and this so-called transcription machinery, can be experimentally manipulated and will unravel the details by which genetic information is expressed. The parts of the transcription machinery studied here are involved in neurological, visual, and immunological diseases.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Sledjeski, Darren D
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Emory University
Schools of Medicine
United States
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Loya, Travis J; O'Rourke, Thomas W; Reines, Daniel (2013) Yeast Nab3 protein contains a self-assembly domain found in human heterogeneous nuclear ribonucleoprotein-C (hnRNP-C) that is necessary for transcription termination. J Biol Chem 288:2111-7
Jenks, M Harley; O'Rourke, Thomas W; Reines, Daniel (2008) Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast. Mol Cell Biol 28:3883-93
Kopcewicz, Katarzyna A; O'Rourke, Thomas W; Reines, Daniel (2007) Metabolic regulation of IMD2 transcription and an unusual DNA element that generates short transcripts. Mol Cell Biol 27:2821-9
Jenks, M Harley; Reines, Daniel (2005) Dissection of the molecular basis of mycophenolate resistance in Saccharomyces cerevisiae. Yeast 22:1181-90
McPhillips, Christine C; Hyle, Judith W; Reines, Daniel (2004) Detection of the mycophenolate-inhibited form of IMP dehydrogenase in vivo. Proc Natl Acad Sci U S A 101:12171-6
Riles, Linda; Shaw, Randal J; Johnston, Mark et al. (2004) Large-scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6-azauracil. Yeast 21:241-8
Hyle, Judith W; Shaw, Randal J; Reines, Daniel (2003) Functional distinctions between IMP dehydrogenase genes in providing mycophenolate resistance and guanine prototrophy to yeast. J Biol Chem 278:28470-8
Reines, Daniel (2003) Use of RNA yeast polymerase II mutants in studying transcription elongation. Methods Enzymol 371:284-92
Shaw, Randal J; Bonawitz, Nicholas D; Reines, Daniel (2002) Use of an in vivo reporter assay to test for transcriptional and translational fidelity in yeast. J Biol Chem 277:24420-6
Wind-Rotolo, M; Reines, D (2001) Analysis of gene induction and arrest site transcription in yeast with mutations in the transcription elongation machinery. J Biol Chem 276:11531-8

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