The Control of Gene Expression by Eukaryotic Ribonucleases

Summary

Principal Investigator: Guillaume F Chanfreau
Abstract: DESCRIPTION (provided by applicant): Degradation of RNA molecules provides a powerful means to control the expression of specific genes. One of the major RNA degradation pathways in eukaryotic cells is the Nonsense-Mediated mRNA decay pathway, which degrades RNA containing premature translation termination codons (PTCs). While the functions of this pathway in eliminating PTC-containing RNAs are well documented, the impact of this pathway in the regulation of expression and the quality control of endogenous transcripts is still unclear. The proposed project will focus on three major functions for NMD in specific gene regulation pathways. First, we will study how NMD can cooperate with other degradation systems to degrade unspliced pre-mRNAs, and the mechanisms that are involved to direct these unspliced RNAs to the different degradation routes. This function is highly critical since accumulation of unspliced pre-mRNAs would result in the production of proteins with deleterious or dominant-negative properties. In addition we will investigate how NMD can regulate the production of alternatively spliced or regulated transcripts. This will include the genomic investigation of transcripts that are spliced at alternative splice sites that include PTCs using RNA-Seq approaches, and understanding how these alternative splicing events are regulated to respond to environmental changes. We have also found an unexpected function for the NMD RNA helicase Upf1p in the control of transcripts specifically spliced or expressed during meiosis and we will investigate the specific role of Upf1p in this process. Finally we found that NMD degrades 5'-extended forms of many genes located within subtelomeric regions, and we have demonstrated that these extended forms mediate the repression of transcription at the bona fide promoters. We will investigate the mechanisms by which these RNAs mediate these repressive functions and the role of NMD in this novel regulatory system. Overall the proposed studies should illustrate the major impact of RNA degradation by NMD in the regulation of gene expression and reveal novel paradigms of gene regulation controlled by this unique RNA quality control pathway. PUBLIC HEALTH RELEVANCE: Mutations that cause genetic diseases often result in premature translation termination codons, which in turn mediate the rapid degradation of mRNAs encoded by these genes by Nonsense Mediated Decay. Genetic Diseases can also result from mutations in splicing signals, which reduce the splicing efficiency or activate cryptic splice sites. Our studies of the turnover of unspliced and mis-spliced RNAs will shed light on the mechanisms by which RNA degradation controls the expression of genes mutated in the context of a large number of genetic diseases.
Funding Period: 2000-07-01 - 2014-06-30
more information: NIH RePORT

Top Publications

  1. pmc Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome
    Defne E Egecioglu
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Box 951569, Los Angeles, CA 90095 1569, USA
    RNA 12:26-32. 2006
  2. pmc RNA polymerase I stability couples cellular growth to metal availability
    Yueh Jung Lee
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095 1569, USA
    Mol Cell 51:105-15. 2013
  3. pmc Intrinsic dynamics of an extended hydrophobic core in the S. cerevisiae RNase III dsRBD contributes to recognition of specific RNA binding sites
    Elon Hartman
    Department of Chemistry and Biochemistry, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 1569, USA
    J Mol Biol 425:546-62. 2013
  4. pmc Sphingolipid signaling mediates iron toxicity
    Yueh Jung Lee
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 1569, USA
    Cell Metab 16:90-6. 2012
  5. pmc Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae
    Shakir Sayani
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
    RNA 18:1563-72. 2012
  6. pmc Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation
    Defne E Egecioglu
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095 1569, USA
    Nucleic Acids Res 40:1787-96. 2012
  7. pmc Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs
    Zhonghua Wang
    Department of Chemistry and Biochemistry, P O Box 951569, University of California, Los Angeles, CA 90095 1569, USA
    Structure 19:999-1010. 2011
  8. pmc Cryptic transcription mediates repression of subtelomeric metal homeostasis genes
    Isabelle Toesca
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 7:e1002163. 2011
  9. pmc Structure of H/ACA RNP protein Nhp2p reveals cis/trans isomerization of a conserved proline at the RNA and Nop10 binding interface
    Bon Kyung Koo
    Department of Chemistry and Biochemistry, and the Molecular Biology Institute, PO Box 951569, University of California, Los Angeles, CA 90095 1569, USA
    J Mol Biol 411:927-42. 2011
  10. pmc Proofreading and spellchecking: a two-tier strategy for pre-mRNA splicing quality control
    Defne E Egecioglu
    Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095 1569, USA
    RNA 17:383-9. 2011

Detail Information

Publications15

  1. pmc Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome
    Defne E Egecioglu
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Box 951569, Los Angeles, CA 90095 1569, USA
    RNA 12:26-32. 2006
    ..These results suggest that polyadenylation of RNA processing intermediates plays a functional role in RNA processing pathways and is not limited to RNA surveillance functions...
  2. pmc RNA polymerase I stability couples cellular growth to metal availability
    Yueh Jung Lee
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095 1569, USA
    Mol Cell 51:105-15. 2013
    ....
  3. pmc Intrinsic dynamics of an extended hydrophobic core in the S. cerevisiae RNase III dsRBD contributes to recognition of specific RNA binding sites
    Elon Hartman
    Department of Chemistry and Biochemistry, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 1569, USA
    J Mol Biol 425:546-62. 2013
    ..These results reveal that dynamics in the extended hydrophobic core are important for binding site selection by the Rnt1p dsRBD...
  4. pmc Sphingolipid signaling mediates iron toxicity
    Yueh Jung Lee
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 1569, USA
    Cell Metab 16:90-6. 2012
    ..These results demonstrate an unexpected connection between sphingolipid flux and iron toxicity and show that activation of a signal transduction cascade contributes to iron-mediated cellular toxicity...
  5. pmc Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae
    Shakir Sayani
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
    RNA 18:1563-72. 2012
    ..The presence of these two sequential degradation pathways for unspliced pre-mRNAs underscores the importance of limiting their accumulation and might serve as a fail-safe mechanism to prevent the expression of these nonfunctional RNAs...
  6. pmc Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation
    Defne E Egecioglu
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA 90095 1569, USA
    Nucleic Acids Res 40:1787-96. 2012
    ....
  7. pmc Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs
    Zhonghua Wang
    Department of Chemistry and Biochemistry, P O Box 951569, University of California, Los Angeles, CA 90095 1569, USA
    Structure 19:999-1010. 2011
    ..Comparison of free and RNA-bound Rnt1p dsRBD reveals that tetraloop-specific binding requires a conformational change in helix α1. Our findings provide a unified model of binding site selection by this dsRBD...
  8. pmc Cryptic transcription mediates repression of subtelomeric metal homeostasis genes
    Isabelle Toesca
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 7:e1002163. 2011
    ....
  9. pmc Structure of H/ACA RNP protein Nhp2p reveals cis/trans isomerization of a conserved proline at the RNA and Nop10 binding interface
    Bon Kyung Koo
    Department of Chemistry and Biochemistry, and the Molecular Biology Institute, PO Box 951569, University of California, Los Angeles, CA 90095 1569, USA
    J Mol Biol 411:927-42. 2011
    ..We propose that Pro83 plays a key role in the assembly of the eukaryotic H/ACA RNP, with the cis conformation locking in a stable Cbf5-Nop10-Nhp2 ternary complex and positioning the protein backbone to interact with the H/ACA RNA...
  10. pmc Proofreading and spellchecking: a two-tier strategy for pre-mRNA splicing quality control
    Defne E Egecioglu
    Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095 1569, USA
    RNA 17:383-9. 2011
    ..The presence of multiple quality control activities during splicing underscores the importance of this process in the expression of genetic information...
  11. pmc Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations
    Tadashi Kawashima
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095 1569, USA
    RNA 15:2236-47. 2009
    ....
  12. pmc Widespread impact of nonsense-mediated mRNA decay on the yeast intronome
    Shakir Sayani
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 1569, USA
    Mol Cell 31:360-70. 2008
    ..These results show that NMD has a wider impact than previously thought on the degradation of yeast-unspliced transcripts and plays an important role in discarding precursors of regulated or suboptimally spliced transcripts...
  13. ncbi Shape-specific recognition in the structure of the Vts1p SAM domain with RNA
    Florian C Oberstrass
    Institute for Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
    Nat Struct Mol Biol 13:160-7. 2006
    ..Using microarray gene profiling, we identified several genes in S. cerevisiae that seem to be regulated by Vts1p and contain one or more copies of the SRE...
  14. pmc Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae
    Tadashi Kawashima
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
    PLoS Genet 10:e1004249. 2014
    ..cerevisiae but masked by RNA degradation and that the use of alternative splice sites in this organism is mostly aimed at controlling transcript levels rather than increasing proteome diversity. ..

Research Grants30

  1. Spatio-temporal dynamics of GEF-GTPase networks
    KLAUS MICHAEL HAHN; Fiscal Year: 2013
    ..abstract_text> ..
  2. Recognition and degradation of mRNA by nonsense-mediated decay
    KRISTIAN EILEEN BAKER; Fiscal Year: 2013
    ..We plan to further challenge this model as well as test our hypothesis that rapid mRNA decay is an indirect consequence of restricting translation initiation factor binding to the mRNA 52 cap. ..
  3. Gene Expression in the Preimplantation Mouse Embryo
    Richard M Schultz; Fiscal Year: 2013
    ..Taken together, results of the proposed studies will generate a detailed understanding of two critical processes that underly the egg-to- embryo transition, i.e., maternal mRNA degradation and reprogramming gene expression. ..
  4. Alternative splicing and nonsense-mediated mRNA decay in neural development
    Sika Zheng; Fiscal Year: 2013
    ..In summary, my educational and research experience together with a strong and supportive mentoring team make me an ideal candidate for this research project and the K99/R00 award. ..
  5. Electron Microscopy of Biological Macromolecules
    Kenneth H Downing; Fiscal Year: 2013
    ....
  6. Pacific Southwest RCE for Biodefense &Emerging Infectious Diseases Research
    Alan G Barbour; Fiscal Year: 2013
    ..abstract_text> ..
  7. Controlling toxic RNA with rapamycin
    JEREMY ROBERT SANFORD; Fiscal Year: 2013
    ....
  8. RNA decay and processing activities of the RNA exosome
    Ambro van Hoof; Fiscal Year: 2013
    ..Our proposed experiments seek to clarify how these helicases assist the exosome in its many function. ..
  9. Histone Chaperones and Acetyltransferases in Chromatin Transitions
    Jennifer K Nyborg; Fiscal Year: 2013
    ..abstract_text> ..
  10. Molecular and Clinical Pharmacology of Retinopathy of Prematurity
    Jacob V Aranda; Fiscal Year: 2013
    ..The NYPD-PRC will surely elevate the level of scientific inquiry on molecular and clinical pharmacology of ROP to hasten its prevention and avert life-long blindness. ..
  11. Mapping Expression Quantitative Trait Loci with Next Generation Sequencing in SLE
    Min Chen; Fiscal Year: 2013
    ....
  12. Mode of Action of a Fragment of hnRNPU in Blocking HIV-1 mRNA Export
    MARK ANTHONY CLEMENTZ; Fiscal Year: 2013
    ..We hope to gain valuable insights into previously unknown aspects in HIV-1 post-integrations steps that might lead to the identification of novel therapeutic avenues. ..
  13. Pacific NorthWest Regional Center of Excellence (PNWRCE)
    Jay A Nelson; Fiscal Year: 2013
    ..pseudomallei host pathogen response during both the septicemic as well as the intracellular phases of the disease. ..
  14. Ty3 viruslike particle morphogenesis and host interactions
    Suzanne Sandmeyer; Fiscal Year: 2013
    ..Huang (UCI) to map interactions within and between cellular VLP, PB, and NPC. The Baldi group (UCI) has expertise in DNA-seq analysis and protein modeling and will collaborate on several aspects of this work. ..
  15. Transcriptome profiling by high throughput RNA Sequencing
    Masoud Toloue; Fiscal Year: 2013
    ....
  16. Regulation of Steroidogenic Genes by Trophic Hormones
    Marion B Sewer; Fiscal Year: 2013
    ..Mass spectrometric analysis of ligands and phospho-specific antibodies will define the relationship between signal-dependent stabilization of the interactions between SF-1 and ligand and SF-1 and coregulatory proteins. ..