JACK KEENE

Summary

Affiliation: Duke University Medical Center
Country: USA

Publications

  1. ncbi request reprint Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays
    Scott A Tenenbaum
    Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Methods 26:191-8. 2002
  2. ncbi request reprint RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nat Protoc 1:302-7. 2006
  3. doi request reprint Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs
    Dale L Beach
    University of North Carolina, Chapel Hill, USA
    Methods Mol Biol 419:69-91. 2008
  4. pmc Coordinated posttranscriptional mRNA population dynamics during T-cell activation
    Neelanjan Mukherjee
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Syst Biol 5:288. 2009
  5. pmc PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
    David L Corcoran
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Genome Biol 12:R79. 2011
  6. pmc RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells
    Luiz O F Penalva
    Department of Molecular Genetics and Microbiology, Center for RNA Biology, 414 Jones Building, Research Drive, Duke University Medical Center, Durham, North Carolina 27710, USA
    Mol Cancer 3:24. 2004
  7. ncbi request reprint RNA regulons: coordination of post-transcriptional events
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Box 3020, Durham, North Carolina 27710, USA
    Nat Rev Genet 8:533-43. 2007
  8. ncbi request reprint Eukaryotic mRNPs may represent posttranscriptional operons
    Jack D Keene
    Center for RNA Biology, Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cell 9:1161-7. 2002
  9. ncbi request reprint Post-transcriptional operons and regulons co-ordinating gene expression
    Jack D Keene
    Center for RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Chromosome Res 13:327-37. 2005
  10. pmc Minireview: global regulation and dynamics of ribonucleic Acid
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Endocrinology 151:1391-7. 2010

Research Grants

Collaborators

  • Scott A Tenenbaum
  • P H King
  • D Antic
  • C V Nicchitta
  • Simon M Lin
  • Isabel Lopez de Silanes
  • R J Maraia
  • Luiz O F Penalva
  • M Gorospe
  • Jennifer L Konopka
  • Neelanjan Mukherjee
  • Patrick J Lager
  • David L Corcoran
  • Adam R Morris
  • Dale L Beach
  • Brook Pyhtila
  • Rachid Mazroui
  • Mary C Reedy
  • Tianli Zheng
  • Samuel B Stephens
  • Daniel J Kenan
  • Robert V Intine
  • Krystyna Mazan-Mamczarz
  • Rachel S Lerner
  • Theophany Eystathioy
  • Rebecca L Skalsky
  • Uwe Ohler
  • Stoyan Georgiev
  • Eva Gottwein
  • F B Gao
  • Matthew B Friedersdorf
  • Marshall A Thompson
  • Imed Eddine Gallouzi
  • Christopher von Roretz
  • Sergio Di Marco
  • Maya Saleh
  • Eveline Clair
  • U Atasoy
  • Joseph W Brewer
  • Rebecca D Dodd
  • Jennifer L Martindale
  • Amy L Sakulich
  • Ulus Atasoy
  • Stefanie Galban
  • Robert M Seiser
  • Edward K L Chan
  • Marvin J Fritzler
  • Kevin Griffith
  • J Watson
  • D Patel
  • C C Query
  • C C Carson
  • D S Harper
  • T Levine
  • L D Fresco
  • S L Deutscher
  • J C Chambers
  • D W Hoffman
  • J B Harley
  • B J Martin
  • R C Bentley
  • D Kenan
  • S W White
  • B L Golden

Detail Information

Publications38

  1. ncbi request reprint Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays
    Scott A Tenenbaum
    Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Methods 26:191-8. 2002
    ..This article describes a series of biochemical techniques that deal with the first two steps of ribonomic profiling: purifying endogenous mRNP complexes and identifying multiple mRNA targets using microarray analysis...
  2. ncbi request reprint RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nat Protoc 1:302-7. 2006
    ..Using RIP-Chip, the identification and/or quantification of RNAs in RNP complexes can be accomplished within a few hours or days depending on the RNA detection method used...
  3. doi request reprint Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs
    Dale L Beach
    University of North Carolina, Chapel Hill, USA
    Methods Mol Biol 419:69-91. 2008
    ..The method was developed in a yeast model system, yet is amenable to other in vivo cell systems including mammalian cell culture...
  4. pmc Coordinated posttranscriptional mRNA population dynamics during T-cell activation
    Neelanjan Mukherjee
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Syst Biol 5:288. 2009
    ..Thus, we describe a strategy to systematically link an RBP and condition-specific posttranscriptional effects to small molecule drugs...
  5. pmc PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
    David L Corcoran
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Genome Biol 12:R79. 2011
    ..Our study describes tailored analytical methods and provides guidelines for future efforts to utilize high-throughput sequencing in RNA biology. PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer/...
  6. pmc RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells
    Luiz O F Penalva
    Department of Molecular Genetics and Microbiology, Center for RNA Biology, 414 Jones Building, Research Drive, Duke University Medical Center, Durham, North Carolina 27710, USA
    Mol Cancer 3:24. 2004
    ....
  7. ncbi request reprint RNA regulons: coordination of post-transcriptional events
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Box 3020, Durham, North Carolina 27710, USA
    Nat Rev Genet 8:533-43. 2007
    ..I close by considering the evolutionary wiring and rewiring of these combinatorial post-transcriptional gene-expression networks...
  8. ncbi request reprint Eukaryotic mRNPs may represent posttranscriptional operons
    Jack D Keene
    Center for RNA Biology, Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cell 9:1161-7. 2002
    ..This model predicts that functionally related genes are regulated posttranscriptionally as groups by specific mRNA binding proteins that recognize sequence elements in common among the mRNAs...
  9. ncbi request reprint Post-transcriptional operons and regulons co-ordinating gene expression
    Jack D Keene
    Center for RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Chromosome Res 13:327-37. 2005
    ....
  10. pmc Minireview: global regulation and dynamics of ribonucleic Acid
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Endocrinology 151:1391-7. 2010
    ....
  11. pmc The global dynamics of RNA stability orchestrates responses to cellular activation
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    BMC Biol 8:95. 2010
    ..A study published recently in BMC Genomics focuses on the contribution made by mRNA stability in shaping the kinetics of gene responses in mammalian cells...
  12. pmc Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome
    J D Keene
    Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 98:7018-24. 2001
    ..Our goal is to understand the organization and flow of genetic information on an integrative systems level by analyzing the collective properties of proteins and mRNAs associated with mRNPs in vivo...
  13. ncbi request reprint Messenger ribonucleoprotein complexes containing human ELAV proteins: interactions with cytoskeleton and translational apparatus
    D Antic
    Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    J Cell Sci 111:183-97. 1998
    ..hELAV proteins in these mRNP granules may affect post-transcriptional regulation of gene expression via the intracellular transport, localization and/or translation of growth regulatory mRNAs...
  14. ncbi request reprint Hel-N1/Hel-N2 proteins are bound to poly(A)+ mRNA in granular RNP structures and are implicated in neuronal differentiation
    F B Gao
    Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    J Cell Sci 109:579-89. 1996
    ..Furthermore, our findings open the possibility that these proteins participate in mRNA homeostasis in the dendrites and soma of mature neurons...
  15. ncbi request reprint Mammalian homologs of Drosophila ELAV localized to a neuronal subset can bind in vitro to the 3' UTR of mRNA encoding the Id transcriptional repressor
    P H King
    Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710
    J Neurosci 14:1943-52. 1994
    ..These findings are interpreted in light of recent studies in which mRNA 3' UTRs were found to be important for the regulation of cell growth and differentiation...
  16. ncbi request reprint A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein
    C C Query
    Department of Microbiology and Immunology, Duke University Medical Center, Durham, North Carolina 27710
    Cell 57:89-101. 1989
    ....
  17. ncbi request reprint ELAV protein HuA (HuR) can redistribute between nucleus and cytoplasm and is upregulated during serum stimulation and T cell activation
    U Atasoy
    Departments of Microbiology, Immunology and Medicine, Duke University Medical Center, Durham, NC 27710 USA
    J Cell Sci 111:3145-56. 1998
    ..This supports the hypothesis that ELAV proteins can function as transacting factors which affect a default pathway of mRNA degradation involved in the expression of growth regulatory proteins...
  18. ncbi request reprint Biological clocks and the coordination theory of RNA operons and regulons
    J D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Cold Spring Harb Symp Quant Biol 72:157-65. 2007
    ....
  19. pmc Molecular analysis of the 60-kDa human Ro ribonucleoprotein
    S L Deutscher
    Department of Microbiology and Immunology, Duke University Medical Center, Durham, NC 27710
    Proc Natl Acad Sci U S A 85:9479-83. 1988
    ..Possible functions of the Ro RNPs and their relationship to RNA polymerase III transcription are discussed...
  20. ncbi request reprint Genomic structure and amino acid sequence domains of the human La autoantigen
    J C Chambers
    Department of Microbiology and Immunology, Duke University Medical Center, Durham, North Carolina 27710
    J Biol Chem 263:18043-51. 1988
    ..These findings support an antigen-driven mechanism for autoimmune reactivity...
  21. pmc RNA binding specificity of a Drosophila snRNP protein that shares sequence homology with mammalian U1-A and U2-B" proteins
    D S Harper
    Department of Microbiology and Immunology, Duke University Medical Center, Durham, NC 27710
    Nucleic Acids Res 20:3645-50. 1992
    ..Furthermore, D25 bound U1 RNA when transfected into mammalian cells. Thus, D25 appears to be a Drosophila homolog of the mammalian U1-A protein, despite its sequence similarity to U2-B"...
  22. ncbi request reprint A human autoimmune protein associated with U1 RNA contains a region of homology that is cross-reactive with retroviral p30gag antigen
    C C Query
    Department of Microbiology and Immunology, Duke University Medical Center, Durham, North Carolina 27710
    Cell 51:211-20. 1987
    ..Thus autoantibodies against U1 snRNPs were elicited by immunization with p30gag. On the basis of these findings, we suggest a role for retroviruses in the initiation of autoimmunity...
  23. pmc RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins
    D W Hoffman
    Department of Microbiology and Immunology, Duke University Medical Center, Durham, NC 27710
    Proc Natl Acad Sci U S A 88:2495-9. 1991
    ..The secondary structure and topology of the RRM are similar to those of ribosomal proteins L12 and L30, suggesting a distant evolutionary relationship between these two types of RNA-associated proteins...
  24. pmc Selection of a subset of mRNAs from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1
    F B Gao
    Department of Microbiology, Duke University Medical Center, Durham, NC 27710
    Proc Natl Acad Sci U S A 91:11207-11. 1994
    ..This approach provides a means to gain access to novel genes expressed in various cell types by partitioning mRNAs containing common sequence elements using RNA-binding proteins...
  25. pmc Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets
    Adam R Morris
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Mol Cell Biol 28:4093-103. 2008
    ....
  26. pmc A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles
    Theophany Eystathioy
    Department of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
    Mol Biol Cell 13:1338-51. 2002
    ..We propose that the GW ribonucleoprotein complex is involved in the posttranscriptional regulation of gene expression by sequestering a specific subset of gene transcripts involved in cell growth and homeostasis...
  27. ncbi request reprint Organizing mRNA export
    Jack D Keene
    Nat Genet 33:111-2. 2003
  28. ncbi request reprint Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera
    Scott A Tenenbaum
    Center for RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Gene 317:79-87. 2003
    ..We demonstrate how these approaches can reduce transcriptomic complexity by partitioning mRNAs into biologically relevant subsets in order to derive information about the expression of multiple, but functionally linked, genes...
  29. ncbi request reprint La gets its wings
    Daniel J Kenan
    Nat Struct Mol Biol 11:303-5. 2004
  30. ncbi request reprint Gene expression analysis of messenger RNP complexes
    Luiz O F Penalva
    The Center For RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    Methods Mol Biol 257:125-34. 2004
    ..This chapter describes techniques for purifying mRNA-protein complexes (mRNPs) and identifying the associated mRNAs..
  31. ncbi request reprint Posttranscriptional generation of macromolecular complexes
    Jack D Keene
    Center for RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Cell 12:1347-9. 2003
    ..recently reported that pre-mRNAs encoding components of inhibitory synapses are bound to neuron-specific Nova RNA-binding proteins...
  32. pmc A two-phase innate host response to alphavirus infection identified by mRNP-tagging in vivo
    Jennifer L Konopka
    Department of Microbiology and Immunology University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
    PLoS Pathog 3:e199. 2007
    ..Our findings suggest that the application of viral mRNP-tagging systems, as introduced here, will facilitate a much more detailed understanding of the highly coordinated host response to infectious agents...
  33. pmc Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum
    Brook Pyhtila
    Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
    RNA 14:445-53. 2008
    ..Combined, these data indicate that the mRNA localization to the ER can be conferred independent of the signal sequence/SRP pathway and suggest that mRNA localization to the ER may utilize cis-encoded targeting information...
  34. pmc Caspase-mediated cleavage of HuR in the cytoplasm contributes to pp32/PHAP-I regulation of apoptosis
    Rachid Mazroui
    Department of Biochemistry, McGill University Health Center, McGill University, Montreal, Quebec H3G 146, Canada
    J Cell Biol 180:113-27. 2008
    ..Thus, we propose a model in which HuR association with pp32/PHAP-I and its caspase-mediated cleavage constitutes a regulatory step that contributes to an amplified apoptotic response...
  35. pmc Stable ribosome binding to the endoplasmic reticulum enables compartment-specific regulation of mRNA translation
    Samuel B Stephens
    Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
    Mol Biol Cell 16:5819-31. 2005
    ..These studies demonstrate that ribosome release from the ER is termination independent and identify new and unexpected roles for the ER compartment in the translational response to induction of the unfolded protein response...
  36. pmc RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation
    Krystyna Mazan-Mamczarz
    Laboratory of Cellular and Molecular Biology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
    Proc Natl Acad Sci U S A 100:8354-9. 2003
    ..Our results demonstrate a role for HuR in binding to the p53 mRNA and enhancing its translation...
  37. pmc Partitioning and translation of mRNAs encoding soluble proteins on membrane-bound ribosomes
    Rachel S Lerner
    Departments of Cell Biology and Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    RNA 9:1123-37. 2003
    ....
  38. ncbi request reprint Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAs
    Robert V Intine
    Laboratory of Molecular Growth Regulation, National Institute of Child Health and Development, Bethesda, MD 20892, USA
    Mol Cell 12:1301-7. 2003
    ....

Research Grants10

  1. POSTTRANSCRIPTIONAL GENE REGULATION IN T CELL ACTIVATION
    JACK KEENE; Fiscal Year: 2004
    ..In summary, HuR will be examined for RNA recognition specificity and interactions, which govern its effects on the stability or translation of cytokine and ERG mRNAs during T cell activation. ..