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    Thoru Pederson PhD

    TitleProfessor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentBiochemistry and Molecular Pharmacology
    AddressUniversity of Massachusetts Medical School
    377 Plantation Street
    Worcester MA 01605
    Phone508-856-8667
      Other Positions
      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBiochemistry and Molecular Pharmacology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentInterdisciplinary Graduate Program

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentProgram in Cell Dynamics

        Overview 
        Narrative

        Academic Background

        Thoru Pederson received his Ph.D. in Zoology from Syracuse University and was a NIH postdoctoral fellow in the Department of Cell Biology at Albert Einstein College of Medicine.He then joined the Worcester Foundation as a Staff Scientist in Cell Biology and was promoted to President of the institute in 1985. In 1997 the Worcester Foundation merged with UMass Medical School. Dr. Pederson holds the Vitold Arnett Professorship, an endowed position, and is also Associate Vice Provost for Research.

        He has held a Scholar Award from the Leukemia & Lymphoma Society of America and has served on the N.I.H. Cell Biology Study Section, the N.I.H. Molecular Biology Study Section, and the Editorial Board of the Journal of Cell Biology.He currently serves on the editorial board of Molecular Biology of the Cell.He is an Elected Fellow of the American Association for the Advancement of Science and of the American Academy of Microbiology.He has been awarded the Wilhelm Bernhard Medal and also the Medal of Charles University, Prague, for his research in the cell nucleus.He has served as the Chair of the Keith Porter Endowment Fund in Cell Biology, which supports the career development of young cell biologists, and also serves as Chair of the Research Awards Review Committee at the Marine Biological Laboratory, Woods Hole, MA, which evaluates proposals for summer research grants -- again emphasizing young scientists.

        Track record of most recent graduate student:

        Qian Huang was the most recent graduate student to finish in the Pederson laboratory.She post-doc’d in the laboratory of Richard Young at the Whitehead Institute, MIT, and is now a Staff Scientist at the Novartis Research Institute, Cambridge, MA

        Vitold Arnett Professor of Cell Biology

        RNA traffic in eukaryotic cells, RNA processing, RNA-protein interactions, microRNAs

        Dr.  Thoru Pederson, Ph.D.

        We are investigating the functional significance of specific protein-RNA interactions in eukaryotic gene expression, with particular emphasis on RNA traffic and processing as well as domains in the cell nucleus where these events are set in motion. One axis of this program combines in situ RNA detection methods with novel approaches we have developed for following fluorescent RNA molecules in living mammalian cells. A recent focus has been the assembly of the signal recognition particle, which we have discovered occurs in an unanticipated place in the cell: the nucleolus. This has led us to look into the possibility that this special domain of the nucleus may be doing yet other things, beyond its long-known role in making ribosomes. We have found that the nucleolus harbors numerous proteins involved in cell cycle progression as well as a specific set of microRNAs. We are now trying to sort out the meaning of both of these unexpected discoveries. My laboratory follows the doctrine uttered by a famous biochemist when asked by a reporter how he planned his work, who replied “I follow my nose.”

        Research Funding

        National Science Foundation grant MCB-1051398, “Probing New Dimensions of the Nucleolus”; April 1, 2011-March 31, 2014



        Rotation Projects

        Background for Student Rotation Projects

        See Politz, Hogan and Pederson (2009) and Politz et al. (2005) in the above list. The novel microRNA work may be the most suitable for student rotations.

        Potential Rotation Projects

        Are the nucleolar microRNAs pri-, pre- or mature?

        Are they complexed with other nucleolar RNAs?

        Do the cell cycle related proteins in the nucleolus exist as heterotypic complexes?

        Does the nucleolus of human embryonic stem cells also share these features (which we have so far looked for, and found, only in transformed human cell lines)?

        Can vanadium tagging be used to detect specific proteins by electron microscopy, perhaps exceeding the limitations of immuno-EM?



        Bibliographic 
        selected publications
        List All   |   Timeline
        1. Pederson T. The persistent plausibility of protein synthesis in the nucleus: process, palimpsest or pitfall? Curr Opin Cell Biol. 2013 Aug; 25(4):520-1.
          View in: PubMed
        2. Pederson T. Turning on a Dime: The 75th Anniversary of America's March Against Polio. FASEB J. 2013 Jul; 27(7):2533-5.
          View in: PubMed
        3. Pederson T. Life, redrawn: a memoir of carl R. Woese (1928-2012). FASEB J. 2013 Apr; 27(4):1285-7.
          View in: PubMed
        4. Ma H, Pederson T. The nucleolus stress response is coupled to an ATR-Chk1-mediated G2 arrest. Mol Biol Cell. 2013 May; 24(9):1334-42.
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        5. Tu S, Pederson T, Weng Z. Networking development by Boolean logic. Nucleus. 2013 Mar 1; 4(2):89-91.
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        6. Politz JC, Pederson T. Tracking nuclear poly(a) RNA movement within and among speckle nuclear bodies and the surrounding nucleoplasm. Methods Mol Biol. 2013; 1042:61-71.
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        7. Pederson T. Steroid sonnets: a conversation with seymour lieberman (1916-2012). FASEB J. 2012 Dec; 26(12):4775-7.
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        8. Pederson T. Sense and antisense in biotech: the first antisense DNA company. FASEB J. 2012 Sep; 26(9):3594-601.
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        9. Pederson T. The "study" role of past National Institutes of Health study sections. Mol Biol Cell. 2012 Sep; 23(17):3281-4.
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        10. Pederson T. Nuclear export, enlightened. Proc Natl Acad Sci U S A. 2012 Jun 12; 109(24):9228-9.
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        11. Pederson T. "Tall oaks fallen": Three Pioneers of Chromosome Science. Nucleus. 2012 Mar 1; 3(2):113-4.
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        12. Pederson T. Paul doty and the modern era of DNA as a molecule. FASEB J. 2012 Mar; 26(3):967-8.
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        13. Pederson T. Is chromatin helical? Nat Rev Mol Cell Biol. 2011; 13(1):6.
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        14. Pederson T. Found in translation: crossing the corpus callosum to explain science. FASEB J. 2011 Jul; 25(7):2093-7.
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        15. Pederson T. The nucleus introduced. Cold Spring Harb Perspect Biol. 2011; 3(5).
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        16. Pederson T. Eric Kandel and Charlie Rose: a stylish synapse review of The Brain Series, televised on The Charlie Rose Show, syndicated by the Public Broadcasting System, now available on DVD. FASEB J. 2011 May; 25(5):1438-41.
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        17. Pederson T. The nucleolus. Cold Spring Harb Perspect Biol. 2011; 3(3).
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        18. Pederson T. Regulatory RNAs derived from transfer RNA? RNA. 2010 Oct; 16(10):1865-9.
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        19. Pederson T. "Compact" nuclear domains: Reconsidering the nucleolus. Nucleus. 2010 Jul; 1(5):444-5.
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        20. Pederson T. An olympian protozoan. Nucleus. 2010 Jan; 1(1):2-3.
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        21. Pederson T. Obituary: Paul C. Zamecnik (1912-2009). Nature. 2009 Nov 26; 462(7272):423.
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        22. Politz JC, Hogan EM, Pederson T. MicroRNAs with a nucleolar location. RNA. 2009 Sep; 15(9):1705-15.
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        23. Pederson T. The discovery of eukaryotic genome design and its forgotten corollary--the postulate of gene regulation by nuclear RNA. FASEB J. 2009 Jul; 23(7):2019-21.
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        24. Pederson T, Tsai RY. In search of nonribosomal nucleolar protein function and regulation. J Cell Biol. 2009 Mar 23; 184(6):771-6.
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        25. Ma H, Pederson T. Nucleostemin: a multiplex regulator of cell-cycle progression. Trends Cell Biol. 2008 Dec; 18(12):575-9.
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        26. Ma H, Pederson T. Nucleophosmin is a binding partner of nucleostemin in human osteosarcoma cells. Mol Biol Cell. 2008 Jul; 19(7):2870-5.
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        27. Pederson T. Turning a PAGE: the overnight sensation of SDS-polyacrylamide gel electrophoresis. FASEB J. 2008 Apr; 22(4):949-53.
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        28. Pederson T. As functional nuclear actin comes into view, is it globular, filamentous, or both? J Cell Biol. 2008 Mar 24; 180(6):1061-4.
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        29. Pederson T. Meeting Holly Smith, through two generations of his disciples. Pharos Alpha Omega Alpha Honor Med Soc. 2008; 71(1):48-9.
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        30. Pederson T. Ribosomal protein mutations in Diamond-Blackfan anemia: might they operate upstream from protein synthesis? FASEB J. 2007 Nov; 21(13):3442-5.
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        31. Ma H, Pederson T. Depletion of the nucleolar protein nucleostemin causes G1 cell cycle arrest via the p53 pathway. Mol Biol Cell. 2007 Jul; 18(7):2630-5.
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        32. Pederson T. Counterpoint: Statistical analysis in NIH peer review--identifying innovation. FASEB J. 2007 Feb; 21(2):309-10; discussion 311.
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        33. Politz JC, Zhang F, Pederson T. MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells. Proc Natl Acad Sci U S A. 2006 Dec 12; 103(50):18957-62.
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        34. Pederson T. Diffraction at the Brandenburg G(r)ate. Symposium on the optical analysis of biomolecular machines. EMBO Rep. 2006 Dec; 7(12):1202-5.
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        35. Ritland Politz JC, Tuft RA, Pederson T. Photoactivation-based labeling and in vivo tracking of RNA molecules in the nucleus. CSH Protoc. 2006; 2006(6).
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        36. Pederson T. Reflections on the prize of prizes: Alfred Nobel. FASEB J. 2006 Nov; 20(13):2186-9.
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        37. Pederson T. The sea urchin's siren. Dev Biol. 2006 Dec 1; 300(1):9-14.
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        38. Pederson T. New surprises in genetic coding and how an ingenious experiment was almost scooped, by evolution. FASEB J. 2006 Sep; 20(11):1759-60.
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        39. Pederson T. The centrosome: built on an mRNA? Nat Cell Biol. 2006 Jul; 8(7):652-4.
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        40. Pederson T. Author, author burning bright; author, author are you right? FASEB J. 2006 Apr; 20(6):600.
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        41. Politz JC, Tuft RA, Prasanth KV, Baudendistel N, Fogarty KE, Lifshitz LM, Langowski J, Spector DL, Pederson T. Rapid, diffusional shuttling of poly(A) RNA between nuclear speckles and the nucleoplasm. Mol Biol Cell. 2006 Mar; 17(3):1239-49.
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        42. Pederson T. 50 years ago protein synthesis met molecular biology: the discoveries of amino acid activation and transfer RNA. FASEB J. 2005 Oct; 19(12):1583-4.
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        43. Pederson T, Aebi U. Nuclear actin extends, with no contraction in sight. Mol Biol Cell. 2005 Nov; 16(11):5055-60.
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        44. Politz JC, Polena I, Trask I, Bazett-Jones DP, Pederson T. A nonribosomal landscape in the nucleolus revealed by the stem cell protein nucleostemin. Mol Biol Cell. 2005 Jul; 16(7):3401-10.
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        45. Sommerville J, Brumwell CL, Politz JC, Pederson T. Signal recognition particle assembly in relation to the function of amplified nucleoli of Xenopus oocytes. J Cell Sci. 2005 Mar 15; 118(Pt 6):1299-307.
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        46. Pederson T. The spatial organization of the genome in mammalian cells. Curr Opin Genet Dev. 2004 Apr; 14(2):203-9.
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        47. Pederson T. Can telomerase be put in its place? J Cell Biol. 2004 Mar 1; 164(5):637-9.
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        48. Alavian CN, Politz JC, Lewandowski LB, Powers CM, Pederson T. Nuclear export of signal recognition particle RNA in mammalian cells. Biochem Biophys Res Commun. 2004 Jan 9; 313(2):351-5.
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        49. Pederson T. The molecular cytology of gene expression: fluorescent RNA as both a stain and tracer in vivo. Eur J Histochem. 2004; 48(1):57-64.
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        50. Pederson T. RNA interference and mRNA silencing, 2004: how far will they reach? Mol Biol Cell. 2004 Feb; 15(2):407-10.
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        51. Politz JC, Tuft RA, Pederson T. Diffusion-based transport of nascent ribosomes in the nucleus. Mol Biol Cell. 2003 Dec; 14(12):4805-12.
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        52. Wang C, Politz JC, Pederson T, Huang S. RNA polymerase III transcripts and the PTB protein are essential for the integrity of the perinucleolar compartment. Mol Biol Cell. 2003 Jun; 14(6):2425-35.
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        53. O'Brien TP, Bult CJ, Cremer C, Grunze M, Knowles BB, Langowski J, McNally J, Pederson T, Politz JC, Pombo A, Schmahl G, Spatz JP, van Driel R. Genome function and nuclear architecture: from gene expression to nanoscience. Genome Res. 2003 Jun; 13(6A):1029-41.
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        54. Pederson T. Historical review: an energy reservoir for mitosis, and its productive wake. Trends Biochem Sci. 2003 Mar; 28(3):125-9.
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        55. Pederson T. Dynamics and genome-centricity of interchromatin domains in the nucleus. Nat Cell Biol. 2002 Dec; 4(12):E287-91.
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        56. Politz JC, Lewandowski LB, Pederson T. Signal recognition particle RNA localization within the nucleolus differs from the classical sites of ribosome synthesis. J Cell Biol. 2002 Nov 11; 159(3):411-8.
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        57. Pederson T, Aebi U. Actin in the nucleus: what form and what for? J Struct Biol. 2002 Oct-Dec; 140(1-3):3-9.
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        58. Mougin A, Torterotot F, Branlant C, Jacobson MR, Huang Q, Pederson T. A 3'-terminal minihelix in the precursor of human spliceosomal U2 small nuclear RNA. J Biol Chem. 2002 Jun 28; 277(26):23137-42.
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        59. Pederson T. Proteomics of the nucleolus: more proteins, more functions? Trends Biochem Sci. 2002 Mar; 27(3):111-2.
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        60. Pederson T. A century of DNA reaches the bedside. Pharos Alpha Omega Alpha Honor Med Soc. 2002; 65(3):27-32.
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        61. Yarovoi SV, Pederson T. Human cell lines expressing hormone regulated T7 RNA polymerase localized at distinct intranuclear sites. Gene. 2001 Sep 5; 275(1):73-81.
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        62. Pederson T. Protein mobility within the nucleus--what are the right moves? Cell. 2001 Mar 9; 104(5):635-8.
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        63. Pederson T. Fluorescent RNA cytochemistry: tracking gene transcripts in living cells. Nucleic Acids Res. 2001 Mar 1; 29(5):1013-6.
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        64. Pederson T. Viewing the ribosome and visiting the nucleolus at Lake Tahoe. RNA. 2001 Jan; 7(1):1-4.
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        65. Politz JC, Pederson T. Review: movement of mRNA from transcription site to nuclear pores. J Struct Biol. 2000 Apr; 129(2-3):252-7.
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        66. Pederson T, Politz JC. The nucleolus and the four ribonucleoproteins of translation. J Cell Biol. 2000 Mar 20; 148(6):1091-5.
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        67. Pederson T. Half a century of "the nuclear matrix". Mol Biol Cell. 2000 Mar; 11(3):799-805.
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        68. Politz JC, Yarovoi S, Kilroy SM, Gowda K, Zwieb C, Pederson T. Signal recognition particle components in the nucleolus. Proc Natl Acad Sci U S A. 2000 Jan 4; 97(1):55-60.
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        69. Pederson T. Movement and localization of RNA in the cell nucleus. FASEB J. 1999 Dec; 13 Suppl 2:S238-42.
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        70. Pederson T. The immunome. Mol Immunol. 1999 Oct-Nov; 36(15-16):1127-8.
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        71. Politz JC, Tuft RA, Pederson T, Singer RH. Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr Biol. 1999 Mar 25; 9(6):285-91.
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        72. Huang Q, Pederson T. A human U2 RNA mutant stalled in 3' end processing is impaired in nuclear import. Nucleic Acids Res. 1999 Feb 15; 27(4):1025-31.
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        73. Pederson T. Growth factors in the nucleolus? J Cell Biol. 1998 Oct 19; 143(2):279-81.
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        74. Pederson T. The plurifunctional nucleolus. Nucleic Acids Res. 1998 Sep 1; 26(17):3871-6.
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        75. Jacobson MR, Pederson T. Localization of signal recognition particle RNA in the nucleolus of mammalian cells. Proc Natl Acad Sci U S A. 1998 Jul 7; 95(14):7981-6.
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        76. Politz JC, Browne ES, Wolf DE, Pederson T. Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc Natl Acad Sci U S A. 1998 May 26; 95(11):6043-8.
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        77. Welton AF, Pederson TC, Buege JA, Aust SD. The molecular weight of NADPH-cytochrome C reductase isolated by immunoprecipitation from detergent-solubilized rat liver microsomes. Biochem Biophys Res Commun. 1973 Sep 5; 54(1):161-7.
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        78. Pederson TC, Aust SD. The role of superoxide and singlet oxygen in lipid peroxidation promoted by xanthine oxidase. Biochem Biophys Res Commun. 1973 Jun 8; 52(3):1071-8.
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        79. Pederson TC, Aust SD. NADPH-dependen lipid peroxidation catalyzed by purified NADPH-cytochrome C reductase from rat liver microsomes. Biochem Biophys Res Commun. 1972 Aug 21; 48(4):789-95.
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        80. Aust SD, Roerig DL, Pederson TC. Evidence for superoxide generation by NADPH-cytochrome c reductase of rat liver microsomes. Biochem Biophys Res Commun. 1972 Jun 9; 47(5):1133-7.
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