D R Morris

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. ncbi The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders
    G Lynn Law
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Genome Biol 6:R111. 2005
  2. ncbi Ribosomal footprints on a transcriptome landscape
    David R Morris
    Department of Biochemistry, University of Washington, Seattle, WA 98195 7350, USA
    Genome Biol 10:215. 2009
  3. ncbi The upstream open reading frame of the mRNA encoding S-adenosylmethionine decarboxylase is a polyamine-responsive translational control element
    H Ruan
    Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington 98195, USA
    J Biol Chem 271:29576-82. 1996
  4. ncbi Cell-specific translational regulation of S-adenosylmethionine decarboxylase mRNA. Dependence on translation and coding capacity of the cis-acting upstream open reading frame
    J R Hill
    Department of Biochemistry, University of Washington, Seattle 98195
    J Biol Chem 268:726-31. 1993
  5. ncbi A mammalian sequence-dependent upstream open reading frame mediates polyamine-regulated translation in yeast
    G J Mize
    Department of Biochemistry, University of Washington, Seattle 98195-7350, USA
    RNA 7:374-81. 2001
  6. ncbi Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase
    G L Law
    Department of Biochemistry, University of Washington, Seattle, 98195-7350, USA
    J Biol Chem 276:38036-43. 2001
  7. ncbi Transcription factor ZBP-89 regulates the activity of the ornithine decarboxylase promoter
    G L Law
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    J Biol Chem 273:19955-64. 1998
  8. ncbi Role of the transcription activator Ste12p as a repressor of PRY3 expression
    Kellie S Bickel
    Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
    Mol Cell Biol 26:7901-12. 2006
  9. ncbi The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae
    Kyle A Serikawa
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Mol Cell Proteomics 2:191-204. 2003
  10. ncbi Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone
    Vivian L MacKay
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Mol Cell Proteomics 3:478-89. 2004

Research Grants

  1. GROWTH REGULATION OF POLYAMINE SYNTHESIS
    David Morris; Fiscal Year: 1991
  2. GROWTH REGULATION OF POLYAMINE SYNTHESIS
    David Morris; Fiscal Year: 1993
  3. GROWTH REGULATION OF POLYAMINE SYNTHESIS
    David Morris; Fiscal Year: 2001
  4. DEVELOPMENT OF TRANSLATION STATE ARRAY ANALYSIS
    David Morris; Fiscal Year: 2003
  5. TRANSLATIONAL CONTROL OF ONCOPROTEIN MDM2 SYNTHESIS
    David Morris; Fiscal Year: 2003
  6. Cell-specific Transcript Profiling in Complex Tissues
    David Morris; Fiscal Year: 2007

Collaborators

  • G Lynn Law
  • L P Zhao
  • A E Pegg
  • J R Yates
  • H Itoh
  • Ruedi H Aebersold
  • C K Abrass
  • Mark R Flory
  • Richard J Fox
  • Kellie S Bickel
  • Vivian L MacKay
  • Kyle A Serikawa
  • Valerie Schaeffer
  • Elisenda Sanz
  • Prabha Sampath
  • G J Mize
  • Nadav Skjøndal-Bar
  • Eileen Turcott
  • Xiaoping Jin
  • Gregory J Mize
  • Alexa Raney
  • Kim M Hansen
  • Linghai Yang
  • G Stanley McKnight
  • Thomas Su
  • Paul S Amieux
  • David K Pritchard
  • Lil Pabon
  • Charles E Murry
  • Stephen M Schwartz
  • Hans Reinecke
  • A J Link
  • X L Xu
  • David R Goodlett
  • Xiaohong Li
  • Hookeun Lee
  • Roger Bumgarner
  • Silvia Englehardt
  • Qin Zong
  • Xie Lillian Xu
  • H Ruan
  • J R Hill
  • D M Schieltz
  • B M Garvik
  • J Eng
  • E Carmack
  • G S Chatta
  • L M Shantz
  • J A Ledbetter
  • S Chang
  • P S Linsley
  • A G Spies
  • R L Kaspar
  • H Cranston
  • T Kakegawa
  • M W White

Detail Information

Publications23

  1. ncbi The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders
    G Lynn Law
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Genome Biol 6:R111. 2005
    ..Unexpectedly, a high frequency of these transcripts showed the appearance of altered 5' leaders that coincide with increased ribosome loading...
  2. ncbi Ribosomal footprints on a transcriptome landscape
    David R Morris
    Department of Biochemistry, University of Washington, Seattle, WA 98195 7350, USA
    Genome Biol 10:215. 2009
    ..Next-generation massively parallel sequencing technology provides a powerful new means of assessing rates and regulation of translation across an entire transcriptome...
  3. ncbi The upstream open reading frame of the mRNA encoding S-adenosylmethionine decarboxylase is a polyamine-responsive translational control element
    H Ruan
    Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington 98195, USA
    J Biol Chem 271:29576-82. 1996
    ..We propose that polyamines do not modulate the rate of recognition of the uORF but rather regulate interaction of the peptide product of the uORF with its target...
  4. ncbi Cell-specific translational regulation of S-adenosylmethionine decarboxylase mRNA. Dependence on translation and coding capacity of the cis-acting upstream open reading frame
    J R Hill
    Department of Biochemistry, University of Washington, Seattle 98195
    J Biol Chem 268:726-31. 1993
    ..Structural features of the carboxyl-terminal 3 amino acids of the putative hexapeptide govern the interaction of the peptide with a component of the translation machinery...
  5. ncbi A mammalian sequence-dependent upstream open reading frame mediates polyamine-regulated translation in yeast
    G J Mize
    Department of Biochemistry, University of Washington, Seattle 98195-7350, USA
    RNA 7:374-81. 2001
    ..Rather, it seems likely that polyamines may be directly participating in an interaction between the uORF-encoded peptide and a constitutive component of the translation machinery, which leads to inhibition of ribosome activity...
  6. ncbi Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase
    G L Law
    Department of Biochemistry, University of Washington, Seattle, 98195-7350, USA
    J Biol Chem 276:38036-43. 2001
    ..These observations are consistent with a model in which regulation of ribosome pausing at the uORF by polyamines controls ribosome access to the downstream AdoMetDC reading frame...
  7. ncbi Transcription factor ZBP-89 regulates the activity of the ornithine decarboxylase promoter
    G L Law
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    J Biol Chem 273:19955-64. 1998
    ..ZBP-89 inhibited the activation of the ornithine decarboxylase promoter by Sp1 in Schneider's Drosophila line 2, consistent with properties previously attributed to NF-ODC1...
  8. ncbi Role of the transcription activator Ste12p as a repressor of PRY3 expression
    Kellie S Bickel
    Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
    Mol Cell Biol 26:7901-12. 2006
    ..PRY3 regulation provides a model for the coordination of both inductive and repressive activities within a regulatory network...
  9. ncbi The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae
    Kyle A Serikawa
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Mol Cell Proteomics 2:191-204. 2003
    ....
  10. ncbi Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone
    Vivian L MacKay
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Mol Cell Proteomics 3:478-89. 2004
    ..These observations underscore that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions...
  11. ncbi Direct analysis of protein complexes using mass spectrometry
    A J Link
    Department of Molecular Biotechnology, University of Washington, Seattle 98195, USA
    Nat Biotechnol 17:676-82. 1999
    ..By offering the ability to identify >100 proteins in a single run, this process enables components in even the largest macromolecular complexes to be analyzed comprehensively...
  12. ncbi Cell-specific translation of S-adenosylmethionine decarboxylase mRNA. Regulation by the 5' transcript leader
    J R Hill
    Department of Biochemistry, University of Washington, Seattle 98195
    J Biol Chem 267:21886-93. 1992
    ..Mutations that remove the uORF, or prevent its initiation, abolish the translational suppression in T cells, establishing that the uORF is a negative element that modulates the cell-specific polysomal distribution of AdoMetDC mRNA...
  13. ncbi Regulated translation termination at the upstream open reading frame in s-adenosylmethionine decarboxylase mRNA
    Alexa Raney
    Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA
    J Biol Chem 277:5988-94. 2002
    ..This regulation may involve an interaction between the peptide, polyamines, and a target in the translational apparatus...
  14. ncbi Silencing the transcriptome's dark matter: mechanisms for suppressing translation of intergenic transcripts
    Kellie S Bickel
    Department of Biochemistry, University of Washington, Box 357350, Seattle, 98133, USA
    Mol Cell 22:309-16. 2006
    ..A variety of mechanisms exist to prevent adventitious production of proteins from these transcripts, ranging from degradation within the nucleus to translational silencing in the cytosol...
  15. ncbi Differential regulation of proto-oncogenes c-jun and c-fos in T lymphocytes activated through CD28
    G S Chatta
    Department of Biochemistry, University of Washington, Seattle 98195
    J Immunol 153:5393-401. 1994
    ..A mechanism is suggested whereby expression of c-jun and junB, in the absence of members of the fos family, can prevent inappropriate activation of T cells caused by ligation of CD28 in the absence of a specific antigenic stimulus...
  16. ncbi Reductions in laminin beta2 mRNA translation are responsible for impaired IGFBP-5-mediated mesangial cell migration in the presence of high glucose
    Valerie Schaeffer
    Primary and Specialty Care Medicine, Department of Veterans Affairs Puget Sound Health Care System, University of Washington School of Medicine, Seattle, Washington 98109, USA
    Am J Physiol Renal Physiol 298:F314-22. 2010
    ....
  17. ncbi A hierarchical network controls protein translation during murine embryonic stem cell self-renewal and differentiation
    Prabha Sampath
    Department of Pathology, Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109, USA
    Cell Stem Cell 2:448-60. 2008
    ..Parsimonious translation in pluripotent state and hierarchical translational regulation during differentiation may be important quality controls for self-renewal and choice of fate in ESCs...
  18. ncbi The two upstream open reading frames of oncogene mdm2 have different translational regulatory properties
    Xiaoping Jin
    Department of Biochemistry, University of Washington, Seattle, Washington 98195 7350, USA
    J Biol Chem 278:25716-21. 2003
    ..The occurrence of two uORFs with differing activities in both the human gene and the mouse orthologue suggests that this pair of elements may play a fundamental role in regulating expression of the mdm2 gene...
  19. ncbi A regulatory cis element and a specific binding factor involved in the mitogenic control of murine ribosomal protein L32 translation
    R L Kaspar
    Department of Biochemistry, University of Washington, Seattle 98195
    J Biol Chem 267:508-14. 1992
    ..This protein is a member of what may be an emerging family of polyribopyrimidine-binding proteins with diverse biochemical functions...
  20. ncbi PSGL-1 and mTOR regulate translation of ROCK-1 and physiological functions of macrophages
    Richard Fox
    Department of Pathology, University of Washington, Seattle, WA 98109, USA
    EMBO J 26:505-15. 2007
    ....
  21. ncbi Cell-type-specific isolation of ribosome-associated mRNA from complex tissues
    Elisenda Sanz
    Department of Biochemistry, University of Washington, Seattle, WA 9819, USA
    Proc Natl Acad Sci U S A 106:13939-44. 2009
    ..We demonstrate the application of this technique in brain using neuron-specific Cre recombinase-expressing mice and in testis using a Sertoli cell Cre recombinase-expressing mouse...
  22. ncbi Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents
    Mark R Flory
    Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
    Proteomics 6:6146-57. 2006
    ..cerevisiae proteins, and will enable further development of technologies for global proteomic analysis of higher eukaryotes...
  23. ncbi Dynamic model of the process of protein synthesis in eukaryotic cells
    Nadav Skjøndal-Bar
    Department for Engineering Cybernetics, Norwegian University of Science and Technology, Trondheim, Norway
    Bull Math Biol 69:361-93. 2007
    ..A novel approach for modeling the elongation process permits useful prediction of protein production and consumption of energy and amino acids, as well as ribosome loading rate and ribosome spacing on the mRNA...

Research Grants29

  1. GROWTH REGULATION OF POLYAMINE SYNTHESIS
    David Morris; Fiscal Year: 1991
    ..In addition, we will further characterize the mechanism of the control of translation of both ODC and SDC mRNAs through the use of in vitro mutagenesis and gene transfer techniques...
  2. GROWTH REGULATION OF POLYAMINE SYNTHESIS
    David Morris; Fiscal Year: 1993
    ..The objective of the proposed studies is to define the mechanism by which upstream open reading frames are involved in regulating translation of AdoMetDC mRNA in particular and transcripts from growth-related genes generally...
  3. GROWTH REGULATION OF POLYAMINE SYNTHESIS
    David Morris; Fiscal Year: 2001
    ..These studies will not only define the mechanism of regulation of a key step in polyamine biosynthesis, but will also extend our fundamental knowledge of the role uORFs in translational control generally. ..
  4. DEVELOPMENT OF TRANSLATION STATE ARRAY ANALYSIS
    David Morris; Fiscal Year: 2003
    ..This study will provide more finely honed high-throughput tools to provide insight into both mechanisms of regulation of individual genes and the levels and activities of the proteins that ultimately dictate phenotype. ..
  5. TRANSLATIONAL CONTROL OF ONCOPROTEIN MDM2 SYNTHESIS
    David Morris; Fiscal Year: 2003
    ..The sequences in the S-mdm2 mRNA that are responsible for the differences in its translation between normal and tumor cells will also be defined. ..
  6. Cell-specific Transcript Profiling in Complex Tissues
    David Morris; Fiscal Year: 2007
    ..The purpose of the proposed research is to test the efficacy of this concept, which has broad applicability in research areas such as host responses to infectious disease, cancer biology and neurobiology. ..