Thoru Pederson, Ph.D.

Academic Role: Professor

Faculty Appointment(s) In:
   Biochemistry and Molecular Pharmacology

Other Affiliation(s):
   Cell Dynamics Group
   Interdisciplinary Graduate Program

Vitold Arnett Professor of Cell Biology

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

We are investigating the functional significance of specific protein-RNA interactions in eukaryotic gene expression, with particular emphasis on RNA traffic and processing.  We have also been combining in situ RNA detection methods with novel approaches we have developed for following fluorescent RNA molecules in living mammalian cells.  One current focus is the assembly of the signal recognition particle.  We are also studying the transport of various RNAs within the nucleus (see video link below).  Another major project concerns novel functions of the nucleolus (beyond its role in ribosome production), with particular emphasis on cell cycle progression and checkpoints.

Selected Recent Publications

Politz, J.C.R., F. Zhang and T. Pederson. (2006)  miR-206 co-localizes with ribosome-rich regions in the nucleolus and cytoplasm of rat myogenic cells.  Proc. Natl. Acad. Sci. USA 103: 18957-18962.  17135348

Ritland Poland, J.C., I. Polena, I. Trask, D.P. Bazett-Jones and T. Pederson. (2005) A non-ribosomal landscape in the nucleolus revealed by the stem cell protein nucleostemin. Mol.Biol.Cell, 16: 3401-3410.  15857956

Sommerville, J., C.L. Brumwell, Ritland Politz, J.C. and T. Pederson. (2005)   Signal recognition particle assembly in relation to the function of amplified nucleoli in Xenopus oocytes.  J. Cell Sci. 118:1299-1307. 15741230

Politz, J.C., R.A. Tuft, and T. Pederson.   (2004). Photoactivation-based labeling and in vivo tracking of RNA molecules in the nucleus.  In Live Cell Imaging: A Laboratory Manual.  Cold Spring Harbor Laboratory Press, 177-185.

Pederson, T. (2004). The spatial organization of the genome in mammalian cells. Curr. Opin. Genet. Dev.14: 203-209.  15196468

Pederson, T. (2004). Can telomerase be put in its place? J. Cell Biol.164: 637-639.  14993231

Pederson, T. (2004). RNA interference and mRNA silencing, 2004: how far will they reach? Mol. Biol. Cell 15: 407-410.  14657237

Politz, J.C., R.A. Tuft, and T. Pederson (2003). Diffusion-based transport of nascent ribosomes in the nucleus. Mol. Biol. Cell 14: 4805-4812.  12960421

Wang, C., J.C. Politz, T. Pederson and S. Huang (2003). RNA polymerase III transcripts and the PTB protein are essential for the integrity of the perinucleolar compartment. Mol. Biol. Cell 14: 2425-2435.  12808040

Politz, J.C., L.B. Lewandowski and T. Pederson (2002). Signal recognition particle RNA localization within the nucleolus differs from the classical sites of ribosome synthesis. J. Cell Biol. 159: 411-418.  12427865

Mougin, A., F. Torterotot, C. Branlant, M.R. Jacobson, Q. Huang and T. Pederson (2002). A 3'-terminal minihelix in the precursor of human spliceosomal U2 small nuclear RNA. J. Biol. Chem. 277: 23137-23142.  11956214

Yarovoi, S.V. and T. Pederson (2001). Human cell lines expressing hormone regulated T7 RNA polymerase localized at distinct intranuclear sites. Gene 275: 73-81.  11574154

Pederson, T. (2001). Protein mobility within the nucleus -- what are the right moves? Cell 104: 635-638.  11257216

Pederson, T. (2001). Fluorescent RNA cytochemistry: tracking gene transcripts in living cells. Nucleic Acids Res. 29: 1013-1016.  11222750

Pederson, T. (2000). Diffusional protein transport within the nucleus: a message in the medium. Nature Cell Biol. 2: E73-E74.  10806486

Politz, J.C. and T. Pederson (2000). Movement of mRNA from transcription site to nuclear pores. J. Struct. Biol. 129: 252-257.  10806075

Pederson, T. and J.C. Politz (2000). The nucleolus and the four ribonucleoproteins of translation. J. Cell Biol. 148: 1091-1095.  10725320

Pederson, T. (2000). Half a century of “the nuclear matrix”. Mol. Biol. Cell 11: 799-805.  10712500

Politz, J.C., S. Yarovoi, S.M. Kilroy, K. Gowda, C., Zwieb and T. Pederson (2000). Signal recognition particle components in the nucleolus. Proc. Natl. Acad. Sci. USA 97: 55-60.  10618370

Politz, J.C., R.A. Tuft, T. Pederson and R.H. Singer (1999). Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr. Biol. 9:285-291.  10209094

Huang, Q. and T. Pederson (1999). A human U2 RNA mutant stalled in 3' end processing is impaired in nuclear import. Nucleic Acids Res. 27: 1025-1031.  9927735

Pederson, T. (1998). The plurifunctional nucleolus. Nucleic Acids Res. 26: 3871-3876.  9705492

Jacobson, M.R. and T. Pederson (1998). Localization of signal recognition particle RNA in the nucleolus of mammalian cells. Proc. Natl. Acad. Sci.USA 95: 7981-7986.  9653126

Politz, J.C., E.S. Browne, D.E. Wolf and T. Pederson (1998). Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc. Natl. Acad. Sci.USA 95: 6043-6048.  9600914

 Background for Student Rotation Projects

Our studies on how various RNAs are transported within and out of the nucleus involve fluorescent tagging of specific RNAs and tracking their intranuclear movements by high speed microscopy and image processing methods.  The current direction in this project focuses on the newly discovered pre-microRNAs that direct RNA interference, as well as other non-coding, “unconventional” RNAs.  Parallel studies focus on the nucleolus, the classical site of ribosome synthesis but now also known from our work and that of others to have additional functions.  We are investigating the assembly of the signal recognition particle (SRP) in the nucleolus, as well as novel proteins that provocatively visit the nucleolus as part of their functions in cell cycle progression and stem cell biology. 

Potential Rotation Projects

Detection and live cell intranuclear tracking of microRNAs involved in muscle cell differentiation.

Fluorescence resonance energy transfer-based detection of RNA-protein interactions in vivo.

Embryonic stem cell-specific aspects of nuclear organization and RNA-protein dynamics.

Laboratory Personnel

Research Assistant Professor
     Joan C. Ritland Politz, Ph.D. - Research Assistant Professor 

Sr. Research Assistant
       Fan Zhang, B.S. - Research Assistant

Postdoctoral Fellow  
       Hanhui Ma, Ph.D. - Postdoctoral Fellow    

Rotation Student (2005)
      Joel O'Bryan, B.S. – Rotation student (spring 2005)

Summer Students (2004)
     Tsering Choden (summer 2005)
     Ian Trask, Bowdoin College.  (His work resulted in co-authored publication.)

  Recent Rotation Students
     Nuria Sanchez-Velar (Ph.D., UMass. Medical School, 2005)
     Nicole Lucier (nearing completion of her UMass. Medical School Ph.D.)

 Administrative Assistant
    Denise Maclachlan

Academic Background

Thoru Pederson received a 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 this institute in 1985.  In 1997 the Worcester Foundation merged with UMass.   Dr. Pederson holds the Vitold Arnett Professorship at UMass, an endowed position, and is also Associate Vice-Chancellor 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 Minority Affairs Committee of the American Society for Cell Biology, and 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 recently was awarded the Wilhelm Bernhard Medal for his research in the cell nucleus.  He presently serves 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 Fellowships Review Committee at the Marine Biological laboratory, Woods Hole, MA, which evaluates proposals for summer research grants- again emphasizing young scientists.  Beyond his biomedical research career, Dr. Pederson serves on the board of several charitable organizations, including one that funds the healthcare and mental health needs of the uninsured and the safety and good health of children

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

Research Funding
Our research is presently funded by N.I.H. and recently has been funded also by the Human Frontier Science Program  Organization.  In addition, we have just been notified of a new grant from the National Science Foundation .

Office: B4-337
Phone: 508-856-8667
Fax: 508-856-8668
E-mail: Thoru.Pederson@umassmed.edu
Keywords: RNA Biology, Stem Cell Biology, Gene Expression, Nuclear Architecture, RNA Interference (RNAi)

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