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    Melissa J Moore PhD

    TitleProfessor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentBiochemistry and Molecular Pharmacology
    AddressUniversity of Massachusetts Medical School
    364 Plantation Street, LRB-825
    Worcester MA 01605
    Phone508-856-8014
      Other Positions
      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBiochemistry and Molecular Pharmacology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBioinformatics and Computational Biology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentInterdisciplinary Graduate Program

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentMD/PhD Program

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentNeuroscience

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentChemical Biology

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentRNA Therapeutics Institute

        Overview 
        Narrative

        Eleanor Eustis Farrington Chair of Cancer Research, Co-Director RNA and Neuro Therapeutics Institutes (RTI, NTI), Howard Hughes Medical Institute Professor

        Eukaryotic RNA Processing and Metabolism

        melissa moore
        Melissa Moore’s work encompasses a broad array of topics involved in post-transcriptional gene regulation in eukaryotes via mechanisms involving RNA.

        Our research currently focuses on three distinct but interconnected areas involving the basic mechanisms of eukaryotic gene expression: (1) the structure and mechanism of the spliceosome, (2) the effects of nuclear-acquired proteins on cytoplasmic messenger RNA (mRNA) metabolism, and (3) the fate of functionally defective ribosomal RNAs (rRNAs) and mRNAs.

        Introns are incoherent strings of nucleotides that interrupt the coding regions of genes. They are removed from nascent RNA transcripts by the process of precursor mRNA (pre- mRNA) splicing.

        Since the majority of genes in multicellular organisms contain introns, their timely and precise removal is essential for proper gene expression. Most introns are excised by the major spliceosome, a complex macromolecular machine containing five stable, small nuclear RNAs (snRNAs) and a multitude of proteins. The spliceosome must be at once precise (e.g., a 1-nucleotide shift in a splice site will throw the protein-coding region completely out of frame) and adaptable (in humans it must recognize >10^5 different splice site pairs in diverse sequence contexts). In metazoans, the recognition problem is compounded by poor conservation of the sequences defining splice sites and the presence of multiple introns per pre-mRNA. Also, a remarkably high percentage of metazoan pre-mRNAs are subject to alternative splicing, which greatly expands the repertoire of proteins that can be expressed from relatively small genomes.

        A major goal of our research is to elucidate the basic mechanisms by which mammalian spliceosomes accurately identify splice sites in pre-mRNAs and then catalyze intron excision. For some time, our primary focus has been the second step of splicing, wherein the intron is excised and the expressed regions (or exons) are ligated together. Recently we succeeded in purifying, in their native state, spliceosomes poised to perform this reaction. Mass spectrometry revealed more than 100 polypeptides associated with this structure. Using techniques for single-particle image reconstruction from electron micrographs, we obtained an initial three-dimensional structural map to ~30-Å resolution. The structure, with dimensions ~240 x 270 Å, exhibits three major domains connected via a series of bridges and tunnels. Further structural analysis is under way. (This work has been carried out in collaboration with Nikolaus Grigorieff [HHMI, Brandeis University].)

        On the mechanistic front, we have recently developed methodologies for following pre- mRNA splicing at the single-molecule level. All previous in vitro mechanistic studies of splicing have utilized ensemble assays that report only the average behavior of a population. Although such bulk assays have provided a wealth of mechanistic insight, they are ultimately limited in their ability to tease out finer mechanistic details. Over the past two decades, single-molecule techniques that complement ensemble measurements have emerged as powerful tools to elucidate the enzyme mechanism. These approaches permit observation of the stochastic behavior of individual binding and catalytic events. They also allow observation of many individual events that would otherwise go undetected.

        Using a pre-mRNA attached to a glass surface via end and containing fluorescent labels in the 5' exon and intron, we are now able to observe individual splicing events in Saccharomyces cerevisiae extracts, using a multiwavelength total internal reflection fluorescence (TIRF) microscope system developed by Jeff Gelles (Brandeis University) and his colleagues. Chemical biology tools are being used to fluorescently label core spliceosomal proteins and snRNAs, as well as a number of transiently associating splicing factors. This system allows us to analyze the dynamic characteristics of individual spliceosomes in real time. It should provide a new window into previously unaddressable questions regarding spliceosome assembly and internal structural transitions, as well as the comings and goings of key splicing factors. (All of the spliceosome structure and mechanism work is supported by a grant from the National Institutes of Health.)

        Structure and Assembly of the Exon Junction Complex

        In addition to removing introns, the process of pre-mRNA splicing has significant consequences for the subsequent metabolism of the product mRNA. That is, mRNAs produced by splicing are subject to different subcellular localization, different

        efficiencies of translation into proteins, and different decay rates than otherwise identical mRNAs produced from intronless genes. Splicing affects downstream mRNA metabolism by altering the complement of proteins that associate with the mRNA to form an mRNP (mRNA ribonucleoprotein particle). Several years ago, in collaboration with Lynne Maquat (University of Rochester) and Elisa Izaurralde (European Molecular Biology Laboratory, Heidelberg), we showed that spliceosomes stably deposit a complex of proteins (the EJC) on mRNAs at a conserved position 20–24 nucleotides upstream of exon-exon junctions. Such EJCs accompany spliced mRNAs to the cytoplasm, where they are ultimately displaced by the process of translation.

        A major unresolved question regarding the EJC had been how this complex manages to bind so tightly to a specific position on mRNA in what seems to be an entirely RNA structure- and sequence-independent fashion. We solved this mystery by identifying eIF4AIII as the EJC anchor. A member of the DEAD-box family of RNA helicases, eIF4AIII represents a new functional class of such proteins that act as RNA "placeholders" or "clothespins" rather than RNA translocases. Such place-holding DEAD-box proteins could serve as a general means for attaching factors that add functionality to an RNP without requiring any special consensus sequences in the RNA.

        Functional Consequences of EJC Deposition

        As stated above, spliced mRNAs exhibit metabolic fates different from the metabolic fates of mRNAs not produced by splicing. We have been investigating to what extent and by what mechanism(s) EJC deposition contributes to these differences. One area of investigation is the efficiency by which mRNAs are utilized as templates for making proteins. Quantitative analysis revealed that two to three times as many protein molecules are made per spliced mRNA molecule than per identical mRNA molecules not made by splicing. Polysome analysis revealed that spliced mRNAs interact more efficiently with ribosomes, the macromolecular machines that use mRNAs as the blueprints to synthesize proteins, than do unspliced mRNAs. This effect may facilitate the rapid expression of newly made mRNAs by enabling them to outcompete translationally experienced mRNAs (that no longer carry EJCs) for limiting translation initiation factors.

        Recently, in collaboration with Gina Turrigiano (Brandeis University) and Christopher Burge (Massachusetts Institute of Technology), we found that eIF4AIII remains associated with dendritically localized mRNAs in mammalian neurons. eIF4AIII knockdown up-regulates at least two proteins involved in postsynaptic function and markedly increases synaptic strength. Thus eIF4AIII appears to act as a key brake on expression of proteins required for synaptic function. One mechanism for this braking action is via the translation-dependent decay of Arc mRNA, the gene for which contains two conserved introns in its 3'-untranslated region (3'-UTR). This is a highly unusual gene structure in mammals, as EJCs downstream of stop codons trigger nonsense- mediated mRNA decay (NMD). A bioinformatics approach revealed 148 other mammalian genes with this same feature, suggesting that translation-dependent mRNA decay mechanisms such as NMD might be widely employed in mammalian cells as a means to limit the amount of protein produced from certain mRNAs. Curiously, a large number of these genes are expressed in hematopoietic cells, suggesting that some feature of blood cells may particularly favor their evolution there. Future experiments will probe the role of the EJC in modulating expression from some of these new 3'-UTR intron- containing genes.

        Clearance of Nonfunctional Ribosomes

        The ribosome is the most abundant macromolecular machine in the cell. Its highly complex structure, composed of both ribosomal RNAs (rRNAs) and proteins, necessitates an intricate assembly mechanism in which pre-rRNA processing and nucleotide modification are coupled with chaperone-assisted rRNA folding and protein association.

        Although the mechanics of this assembly process are becoming increasingly understood, surprisingly little is known about the mechanisms assuring its overall fidelity. Furthermore, given their inordinately long half-lives in eukaryotic cells, it is to be expected that some ribosomes will become nonfunctional over time as they accumulate oxidative damage due to normal cellular metabolism. We therefore wondered whether eukaryotes might possess any mechanisms for eliminating ribosomes that are fully assembled but functionally defective, akin to their abilities to eliminate mRNAs that are fully processed but defective. To test this, we introduced point mutations into the peptidyltransferase center of 25S rRNA and the decoding center of 18S rRNA in S. cerevisiae. These mutant rRNAs are assembled into ribosomes, but they display markedly decreased steady-state levels compared to wild-type rRNAs.

        Preliminary analyses of knockout strains have revealed several candidate genes important for decreased expression of the translationally defective mutant rRNAs. Our results therefore indicate that budding yeast do contain a quality control system capable of recognizing and eliminating translationally deficient ribosomes so as to prevent their interference with normal cellular function. We continue to study the trans-acting factors and molecular mechanisms involved in this process.

        For more information, visit her Howard Hughes Medical Institute webpage at:
        http://www.hhmi.org/research/investigators/moore_bio.html



        Rotation Projects

        Our laboratory combines biochemical, biophysical, molecular and cell biological approaches to investigate various aspects of pre-mRNA processing, mRNA metabolism and RNA quality control in eukaryotic cells. Potential rotation projects are available in all areas of the laboratory's interests (see Research section).



        Bibliographic 
        selected publications
        List All   |   Timeline
        1. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB, O'Neill LA, Moore MJ, Caffrey DR, Fitzgerald KA. A long noncoding RNA mediates both activation and repression of immune response genes. Science. 2013 Aug 16; 341(6147):789-92.
          View in: PubMed
        2. Li XZ, Roy CK, Moore MJ, Zamore PD. Defining piRNA primary transcripts. Cell Cycle. 2013 Jun 1; 12(11):1657-8.
          View in: PubMed
        3. Jokhi V, Ashley J, Nunnari J, Noma A, Ito N, Wakabayashi-Ito N, Moore MJ, Budnik V. Torsin mediates primary envelopment of large ribonucleoprotein granules at the nuclear envelope. Cell Rep. 2013 Apr 25; 3(4):988-95.
          View in: PubMed
        4. Crawford DJ, Hoskins AA, Friedman LJ, Gelles J, Moore MJ. Single-molecule colocalization FRET evidence that spliceosome activation precedes stable approach of 5' splice site and branch site. Proc Natl Acad Sci U S A. 2013 Apr 23; 110(17):6783-8.
          View in: PubMed
        5. Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD. An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes. Mol Cell. 2013 Apr 11; 50(1):67-81.
          View in: PubMed
        6. Aronin N, Moore M. Hunting down huntingtin. N Engl J Med. 2012 Nov; 367(18):1753-4.
          View in: PubMed
        7. Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ. Introns in UTRs: Why we should stop ignoring them. Bioessays. 2012 Dec; 34(12):1025-34.
          View in: PubMed
        8. Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus. Cell. 2012 Oct 17.
          View in: PubMed
        9. Wu CH, Fallini C, Ticozzi N, Keagle PJ, Sapp PC, Piotrowska K, Lowe P, Koppers M, McKenna-Yasek D, Baron DM, Kost JE, Gonzalez-Perez P, Fox AD, Adams J, Taroni F, Tiloca C, Leclerc AL, Chafe SC, Mangroo D, Moore MJ, Zitzewitz JA, Xu ZS, van den Berg LH, Glass JD, Siciliano G, Cirulli ET, Goldstein DB, Salachas F, Meininger V, Rossoll W, Ratti A, Gellera C, Bosco DA, Bassell GJ, Silani V, Drory VE, Brown RH, Landers JE. Mutations in the profilin 1 gene cause familial amyotrophic lateral sclerosis. Nature. 2012 Aug 22; 488(7412):499-503.
          View in: PubMed
        10. Speese SD, Ashley J, Jokhi V, Nunnari J, Barria R, Li Y, Ataman B, Koon A, Chang YT, Li Q, Moore MJ, Budnik V. Nuclear Envelope Budding Enables Large Ribonucleoprotein Particle Export during Synaptic Wnt Signaling. Cell. 2012 May 11; 149(4):832-46.
          View in: PubMed
        11. Hoskins AA, Moore MJ. The spliceosome: a flexible, reversible macromolecular machine. Trends Biochem Sci. 2012 May; 37(5):179-88.
          View in: PubMed
        12. Morello LG, Coltri PP, Quaresma AJ, Simabuco FM, Silva TC, Singh G, Nickerson JA, Oliveira CC, Moore MJ, Zanchin NI. The Human Nucleolar Protein FTSJ3 Associates with NIP7 and Functions in Pre-rRNA Processing. PLoS One. 2011; 6(12):e29174.
          View in: PubMed
        13. Hoskins AA, Gelles J, Moore MJ. New insights into the spliceosome by single molecule fluorescence microscopy. Curr Opin Chem Biol. 2011 Dec; 15(6):864-70.
          View in: PubMed
        14. Cenik C, Chua HN, Zhang H, Tarnawsky SP, Akef A, Derti A, Tasan M, Moore MJ, Palazzo AF, Roth FP. Genome Analysis Reveals Interplay between 5'UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes. PLoS Genet. 2011 Apr; 7(4):e1001366.
          View in: PubMed
        15. Hoskins AA, Friedman LJ, Gallagher SS, Crawford DJ, Anderson EG, Wombacher R, Ramirez N, Cornish VW, Gelles J, Moore MJ. Ordered and dynamic assembly of single spliceosomes. Science. 2011 Mar 11; 331(6022):1289-95.
          View in: PubMed
        16. Sephton CF, Cenik C, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G. Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. J Biol Chem. 2011 Jan 14; 286(2):1204-15.
          View in: PubMed
        17. Moore MJ, Flotte TR. Autoimmunity in a genetic disease—a cautionary tale. N Engl J Med. 2010 Oct 7; 363(15):1473-5.
          View in: PubMed
        18. Lemmens R, Moore MJ, Al-Chalabi A, Brown RH, Robberecht W. RNA metabolism and the pathogenesis of motor neuron diseases. Trends Neurosci. 2010 May; 33(5):249-58.
          View in: PubMed
        19. Albert BJ, McPherson PA, O'Brien K, Czaicki NL, Destefino V, Osman S, Li M, Day BW, Grabowski PJ, Moore MJ, Vogt A, Koide K. Meayamycin inhibits pre-messenger RNA splicing and exhibits picomolar activity against multidrug-resistant cells. Mol Cancer Ther. 2009 Aug; 8(8):2308-18.
          View in: PubMed
        20. Cole SE, LaRiviere FJ, Merrikh CN, Moore MJ. A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Mol Cell. 2009 May 14; 34(4):440-50.
          View in: PubMed
        21. Moore MJ, Proudfoot NJ. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell. 2009 Feb 20; 136(4):688-700.
          View in: PubMed
        22. Bramham CR, Worley PF, Moore MJ, Guzowski JF. The immediate early gene arc/arg3.1: regulation, mechanisms, and function. J Neurosci. 2008 Nov 12; 28(46):11760-7.
          View in: PubMed
        23. O'Brien K, Matlin AJ, Lowell AM, Moore MJ. The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing. J Biol Chem. 2008 Nov 28; 283(48):33147-54.
          View in: PubMed
        24. Rozovsky N, Butterworth AC, Moore MJ. Interactions between eIF4AI and its accessory factors eIF4B and eIF4H. RNA. 2008 Oct; 14(10):2136-48.
          View in: PubMed
        25. Crawford DJ, Hoskins AA, Friedman LJ, Gelles J, Moore MJ. Visualizing the splicing of single pre-mRNA molecules in whole cell extract. RNA. 2008 Jan; 14(1):170-9.
          View in: PubMed
        26. Giorgi C, Yeo GW, Stone ME, Katz DB, Burge C, Turrigiano G, Moore MJ. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell. 2007 Jul 13; 130(1):179-91.
          View in: PubMed
        27. Giorgi C, Moore MJ. The nuclear nurture and cytoplasmic nature of localized mRNPs. Semin Cell Dev Biol. 2007 Apr; 18(2):186-93.
          View in: PubMed
        28. Matlin AJ, Moore MJ. Spliceosome assembly and composition. Adv Exp Med Biol. 2007; 623:14-35.
          View in: PubMed
        29. LaRiviere FJ, Cole SE, Ferullo DJ, Moore MJ. A late-acting quality control process for mature eukaryotic rRNAs. Mol Cell. 2006 Nov 17; 24(4):619-26.
          View in: PubMed
        30. Stroupe ME, Tange TØ, Thomas DR, Moore MJ, Grigorieff N. The three-dimensional arcitecture of the EJC core. J Mol Biol. 2006 Jul 21; 360(4):743-9.
          View in: PubMed
        31. Shibuya T, Tange TØ, Stroupe ME, Moore MJ. Mutational analysis of human eIF4AIII identifies regions necessary for exon junction complex formation and nonsense-mediated mRNA decay. RNA. 2006 Mar; 12(3):360-74.
          View in: PubMed
        32. Tange TØ, Shibuya T, Jurica MS, Moore MJ. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA. 2005 Dec; 11(12):1869-83.
          View in: PubMed
        33. Schroder PA, Moore MJ. Association of ribosomal proteins with nascent transcripts in S. cerevisiae. RNA. 2005 Oct; 11(10):1521-9.
          View in: PubMed
        34. Moore MJ. From birth to death: the complex lives of eukaryotic mRNAs. Science. 2005 Sep 2; 309(5740):1514-8.
          View in: PubMed
        35. Du H, Tardiff DF, Moore MJ, Rosbash M. Effects of the U1C L13 mutation and temperature regulation of yeast commitment complex formation. Proc Natl Acad Sci U S A. 2004 Oct 12; 101(41):14841-6.
          View in: PubMed
        36. Tange TØ, Nott A, Moore MJ. The ever-increasing complexities of the exon junction complex. Curr Opin Cell Biol. 2004 Jun; 16(3):279-84.
          View in: PubMed
        37. Shibuya T, Tange TØ, Sonenberg N, Moore MJ. eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat Struct Mol Biol. 2004 Apr; 11(4):346-51.
          View in: PubMed
        38. Jurica MS, Sousa D, Moore MJ, Grigorieff N. Three-dimensional structure of C complex spliceosomes by electron microscopy. Nat Struct Mol Biol. 2004 Mar; 11(3):265-9.
          View in: PubMed
        39. Nott A, Le Hir H, Moore MJ. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 2004 Jan 15; 18(2):210-22.
          View in: PubMed
        40. Jurica MS, Moore MJ. Pre-mRNA splicing: awash in a sea of proteins. Mol Cell. 2003 Jul; 12(1):5-14.
          View in: PubMed
        41. Nott A, Meislin SH, Moore MJ. A quantitative analysis of intron effects on mammalian gene expression. RNA. 2003 May; 9(5):607-17.
          View in: PubMed
        42. Le Hir H, Nott A, Moore MJ. How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci. 2003 Apr; 28(4):215-20.
          View in: PubMed
        43. Reichert VL, Le Hir H, Jurica MS, Moore MJ. 5' exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly. Genes Dev. 2002 Nov 1; 16(21):2778-91.
          View in: PubMed
        44. Jurica MS, Moore MJ. Capturing splicing complexes to study structure and mechanism. Methods. 2002 Nov; 28(3):336-45.
          View in: PubMed
        45. Moore MJ. RNA events. No end to nonsense. Science. 2002 Oct 11; 298(5592):370-1.
          View in: PubMed
        46. Jurica MS, Licklider LJ, Gygi SR, Grigorieff N, Moore MJ. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA. 2002 Apr; 8(4):426-39.
          View in: PubMed
        47. Moore MJ. Nuclear RNA turnover. Cell. 2002 Feb 22; 108(4):431-4.
          View in: PubMed
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