RNA polymerase II Elongation Complex: Structure and Function

Summary

Principal Investigator: Daniel Reines
Abstract: DESCRIPTION (provided by applicant): 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.
Funding Period: 1991-07-01 - 2014-07-31
more information: NIH RePORT

Top Publications

  1. pmc Metabolic regulation of IMD2 transcription and an unusual DNA element that generates short transcripts
    Katarzyna A Kopcewicz
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA
    Mol Cell Biol 27:2821-9. 2007
  2. pmc Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast
    M Harley Jenks
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
    Mol Cell Biol 28:3883-93. 2008
  3. pmc A genetic screen for terminator function in yeast identifies a role for a new functional domain in termination factor Nab3
    Travis J Loya
    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
    Nucleic Acids Res 40:7476-91. 2012
  4. ncbi Decapping goes nuclear
    Daniel Reines
    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
    Mol Cell 46:241-2. 2012
  5. pmc Yeast Nab3 protein contains a self-assembly domain found in human heterogeneous nuclear ribonucleoprotein-C (hnRNP-C) that is necessary for transcription termination
    Travis J Loya
    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
    J Biol Chem 288:2111-7. 2013
  6. pmc A network of interdependent molecular interactions describes a higher order Nrd1-Nab3 complex involved in yeast transcription termination
    Travis J Loya
    From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
    J Biol Chem 288:34158-67. 2013

Detail Information

Publications6

  1. pmc Metabolic regulation of IMD2 transcription and an unusual DNA element that generates short transcripts
    Katarzyna A Kopcewicz
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA
    Mol Cell Biol 27:2821-9. 2007
    ..These findings support a model in which intergenic short transcripts emanating from upstream of the IMD2 promoter are terminated by a polyadenylation/terminator-like signal embedded within the IMD2 transcription start site...
  2. pmc Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast
    M Harley Jenks
    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
    Mol Cell Biol 28:3883-93. 2008
    ..These findings extend the emerging concept that distinct modes of termination by RNA polymerase II exist and that the distance of the terminator from the promoter, as well as its sequence, is important for the pathway chosen...
  3. pmc A genetic screen for terminator function in yeast identifies a role for a new functional domain in termination factor Nab3
    Travis J Loya
    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
    Nucleic Acids Res 40:7476-91. 2012
    ..Structural homology modeling suggests this Nab3 'tail' forms an α-helical multimerization domain that helps assemble it onto an RNA substrate...
  4. ncbi Decapping goes nuclear
    Daniel Reines
    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
    Mol Cell 46:241-2. 2012
    ..In this issue of Molecular Cell, Brannan et al. (2012) propose a novel function for RNA-decapping and transcription termination in aborting "divergent" promoter-proximal elongation complexes...
  5. pmc Yeast Nab3 protein contains a self-assembly domain found in human heterogeneous nuclear ribonucleoprotein-C (hnRNP-C) that is necessary for transcription termination
    Travis J Loya
    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
    J Biol Chem 288:2111-7. 2013
    ..This process is independent of, but acts in concert with, the interactions of the proteins with RNA and RNA polymerase and extends the relationship of Nab3 as a functional orthologue of a higher eukaryotic hnRNP...
  6. pmc A network of interdependent molecular interactions describes a higher order Nrd1-Nab3 complex involved in yeast transcription termination
    Travis J Loya
    From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
    J Biol Chem 288:34158-67. 2013
    ..These data strengthen the idea that a multiplicity of interactions is needed to assemble a higher order Nrd1-Nab3 complex that coats specific nascent RNAs in preparation for termination. ..

Research Grants30

  1. Neuronal RNA processing defects in ALS4 caused by SETX mutations
    Craig L Bennett; Fiscal Year: 2013
    ..This underscores the importance of senataxin function in the survival of various neuronal populations. Our studies seek to determine the molecular mechanisms leading to motor neuron loss in ALS4 and further characterize the ..
  2. The RNA polymerase II transcription complex
    Stephen Buratowski; Fiscal Year: 2013
    ..This fundamental knowledge is essential for understanding how mutations in transcription factors and histone modifying enzymes lead to diseases such as cancer and developmental defects. ..
  3. B-cell Biology of Mucosal Immune Protection from SIV Challenge
    Eric Hunter; Fiscal Year: 2013
    ....
  4. Elucidating mechanisms of mitochondrial gene expression at nucleotide resolution
    Mary Couvillion; Fiscal Year: 2013
    ....
  5. MECHANISMS OF TRANSCRIPTIONAL REGULATION IN CHROMATIN
    Jerry L Workman; Fiscal Year: 2013
    ..These studies will reveal fundamental information regarding the process of reassembling chromatin behind RNA polymerase II, which is required to preserve the fidelity of transcription initiation. 1 ..
  6. BIOCHEMISTRY OF EUKARYOTIC MESSENGER RNA SYNTHESIS
    Ronald C Conaway; Fiscal Year: 2013
    ....
  7. Nucleic Acid Enzymes and Nucleic Acids Studied at the Molecular Level
    Steven M Block; Fiscal Year: 2013
    ....
  8. REGULATION OF DNA DAMAGE INDUCED GENES BY YEAST TAFIIS
    Joseph C Reese; Fiscal Year: 2013
    ..The long term goals of this project are to understand how this multi-functional complex regulates multiple steps in gene regulation to maintain normal development and the integrity of the genome in eukaryotic cells. ..
  9. Nucleosome Reorganizing/Remodeling Complexes
    Christopher P Hill; Fiscal Year: 2013
    ..We aim to advance understanding of function by a combination of determining relevant three-dimensional structures, biochemistry, and genetic analysis. ..
  10. Mechanism and targets of Sen1-dependent RNA polymerase II termination
    David A Brow; Fiscal Year: 2013
    ..We will use yeast as model system to explore Sen1 function and better understand how defects in the human Senataxin protein lead to disabling diseases. ..
  11. HORMONAL REGULATION OF BLOOD PRESSURE
    Michal Laniado Schwartzman; Fiscal Year: 2013
    ..ular tone, in the pathophysiology of hypertension and cardiovascular disease. ..
  12. The Role of DEAD-box Proteins in Gene Expression
    Elizabeth J Tran; Fiscal Year: 2013
    ..Knowledge regarding the function of hDDX5 in gene expression is key to defining the underlying molecular basis for cancer and other human diseases. ..
  13. Mechanism and Regulation of RNA Polymerase II Elongation
    Craig D Kaplan; Fiscal Year: 2013
    ..These experiments will reveal the nature of elongation defects in vivo, and how alteration of elongation contributes to gene expression. This work will establish new paradigms for the dissection of Pol II elongation factor function. ..
  14. Spatial and Temporal Regulation of Angiogenesis
    HAROLD FISHER DVORAK; Fiscal Year: 2013
    ..abstract_text> ..
  15. Structural Studies of RNA Maturation and Processing
    Christopher D Lima; Fiscal Year: 2013
    ..Pathways and enzymes that regulate the abundance, lifetime, and processing of RNA have been associated with human diseases that include neurodegenerative disorders, cancer, and inflammation. ..
  16. Visualizing Genetic Activity in Normal &Mutant Yeast
    Ann L Beyer; Fiscal Year: 2013
    ....
  17. Electron Microscopy of Biological Macromolecules
    Kenneth H Downing; Fiscal Year: 2013
    ....
  18. Regulation of transcription termination and its link in mRNA surveillance
    Chi Ming Wong; Fiscal Year: 2013
    ..abstract_text> ..