Research Topics
| JACK KEENESummaryAffiliation: Duke University Medical Center Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arraysScott 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...
Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAsDale 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...
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence dataDavid 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/...- RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cellsLuiz 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.... - The global dynamics of RNA stability orchestrates responses to cellular activationJack 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... - Minireview: global regulation and dynamics of ribonucleic AcidJack D Keene
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
Endocrinology 151:1391-7. 2010.... - Post-transcriptional operons and regulons co-ordinating gene expressionJack 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.... - Eukaryotic mRNPs may represent posttranscriptional operonsJack 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... - RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extractsJack 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... - RNA regulons: coordination of post-transcriptional eventsJack 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... - Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteomeJ 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... - Messenger ribonucleoprotein complexes containing human ELAV proteins: interactions with cytoskeleton and translational apparatusD 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... - Hel-N1/Hel-N2 proteins are bound to poly(A)+ mRNA in granular RNP structures and are implicated in neuronal differentiationF 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... - Mammalian homologs of Drosophila ELAV localized to a neuronal subset can bind in vitro to the 3' UTR of mRNA encoding the Id transcriptional repressorP 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... - A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP proteinC C Query
Department of Microbiology and Immunology, Duke University Medical Center, Durham, North Carolina 27710
Cell 57:89-101. 1989.... - ELAV protein HuA (HuR) can redistribute between nucleus and cytoplasm and is upregulated during serum stimulation and T cell activationU 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... - Biological clocks and the coordination theory of RNA operons and regulonsJ 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.... - Molecular analysis of the 60-kDa human Ro ribonucleoproteinS 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... - Genomic structure and amino acid sequence domains of the human La autoantigenJ 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... - RNA binding specificity of a Drosophila snRNP protein that shares sequence homology with mammalian U1-A and U2-B" proteinsD 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"... - RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteinsD 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... - A human autoimmune protein associated with U1 RNA contains a region of homology that is cross-reactive with retroviral p30gag antigenC 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... - Selection of a subset of mRNAs from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1F 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... - Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune seraScott 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... - Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target setsAdam R Morris
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
Mol Cell Biol 28:4093-103. 2008.... - A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic specklesTheophany 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... - Organizing mRNA exportJack D Keene
Nat Genet 33:111-2. 2003 - Posttranscriptional generation of macromolecular complexesJack 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... - Gene expression analysis of messenger RNP complexesLuiz 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.. - La gets its wingsDaniel J Kenan
Nat Struct Mol Biol 11:303-5. 2004 - Stable ribosome binding to the endoplasmic reticulum enables compartment-specific regulation of mRNA translationSamuel 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... - Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAsRobert V Intine
Laboratory of Molecular Growth Regulation, National Institute of Child Health and Development, Bethesda, MD 20892, USA
Mol Cell 12:1301-7. 2003.... - RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiationKrystyna 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... - A two-phase innate host response to alphavirus infection identified by mRNP-tagging in vivoJennifer 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... - Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulumBrook 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... - Caspase-mediated cleavage of HuR in the cytoplasm contributes to pp32/PHAP-I regulation of apoptosisRachid 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... - Partitioning and translation of mRNAs encoding soluble proteins on membrane-bound ribosomesRachel 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....
Research Grants
- POSTTRANSCRIPTIONAL GENE REGULATION IN T CELL ACTIVATIONJACK 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. ..