James C Carrington

Summary

Affiliation: Oregon State University
Country: USA

Publications

  1. ncbi request reprint Role of microRNAs in plant and animal development
    James C Carrington
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Science 301:336-8. 2003
  2. pmc Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting
    Miya D Howell
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Cell 19:926-42. 2007
  3. pmc Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis
    Josh T Cuperus
    Molecular and Cellular Biology Program, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
    Nat Struct Mol Biol 17:997-1003. 2010
  4. doi request reprint Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation
    Taiowa A Montgomery
    Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    Cell 133:128-41. 2008
  5. pmc Update of ASRP: the Arabidopsis Small RNA Project database
    Tyler W H Backman
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology and Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    Nucleic Acids Res 36:D982-5. 2008
  6. pmc MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Cell 22:1074-89. 2010
  7. pmc High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
    PLoS ONE 2:e219. 2007
  8. pmc Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step
    Elisabeth J Chapman
    Department of Botany and Plant Pathology, and Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Genes Dev 18:1179-86. 2004
  9. pmc Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing
    Josh T Cuperus
    Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    Proc Natl Acad Sci U S A 107:466-71. 2010
  10. ncbi request reprint Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon
    Marin Chiba
    Department of Botany and Plant Pathology and Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
    Virology 346:7-14. 2006

Collaborators

Detail Information

Publications50

  1. ncbi request reprint Role of microRNAs in plant and animal development
    James C Carrington
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Science 301:336-8. 2003
    ..miRNAs are negative regulators that function as specificity determinants, or guides, within complexes that inhibit protein synthesis (animals) or promote degradation (plants) of mRNA targets...
  2. pmc Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting
    Miya D Howell
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Cell 19:926-42. 2007
    ..We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families...
  3. pmc Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis
    Josh T Cuperus
    Molecular and Cellular Biology Program, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
    Nat Struct Mol Biol 17:997-1003. 2010
    ..These data suggest that AGO1 functions differentially with 21- and 22-nt miRNAs to engage the RDR6-associated amplification apparatus...
  4. doi request reprint Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation
    Taiowa A Montgomery
    Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    Cell 133:128-41. 2008
    ..miR390 and AGO7, therefore, evolved as a highly specific miRNA guide/effector protein pair to function at two distinct tasiRNA biogenesis steps...
  5. pmc Update of ASRP: the Arabidopsis Small RNA Project database
    Tyler W H Backman
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology and Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    Nucleic Acids Res 36:D982-5. 2008
    ..New search and visualization tools have also been developed to improve access to small RNA classes and their targets. ASRP is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu/db/...
  6. pmc MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Cell 22:1074-89. 2010
    ..Additionally, target sites of younger miRNA were lost more frequently than for deeply conserved families. In summary, our systematic analyses emphasize the dynamic nature of the MIRNA complement of plant genomes...
  7. pmc High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
    PLoS ONE 2:e219. 2007
    ..We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks...
  8. pmc Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step
    Elisabeth J Chapman
    Department of Botany and Plant Pathology, and Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Genes Dev 18:1179-86. 2004
    ..In addition, p21 bound to synthetic miRNA/miRNA* and siRNA duplexes in vitro. We propose that several different suppressors act by distinct mechanisms to inhibit the incorporation of small RNAs into active RISCs...
  9. pmc Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing
    Josh T Cuperus
    Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
    Proc Natl Acad Sci U S A 107:466-71. 2010
    ....
  10. ncbi request reprint Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon
    Marin Chiba
    Department of Botany and Plant Pathology and Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
    Virology 346:7-14. 2006
    ..The members of this family are predicted to have RNA silencing suppressor activity...
  11. pmc Computational and analytical framework for small RNA profiling by high-throughput sequencing
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
    RNA 15:992-1002. 2009
    ..Computational methods were also developed to rapidly and accurately parse, quantify, and map small RNA data...
  12. ncbi request reprint P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction
    Kristin D Kasschau
    Center for Gene Research and Biotechnology and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Dev Cell 4:205-17. 2003
    ..The basis for TuMV- and other virus-induced disease in plants may be explained, at least partly, by interference with miRNA-controlled developmental pathways that share components with the antiviral RNA-silencing pathway...
  13. ncbi request reprint Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
    Cesar Llave
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Science 297:2053-6. 2002
    ....
  14. pmc Genetic and functional diversification of small RNA pathways in plants
    Zhixin Xie
    Center for Gene Research and Biotechnology and Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
    PLoS Biol 2:E104. 2004
    ..We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense...
  15. pmc DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana
    Zhixin Xie
    Center for Gene Research and Biotechnology and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Proc Natl Acad Sci U S A 102:12984-9. 2005
    ..These data support the concept that plants have specialized and compartmentalized DCL functions for biogenesis of distinct small RNA classes...
  16. pmc AGO1-miR173 complex initiates phased siRNA formation in plants
    Taiowa A Montgomery
    Molecular and Cellular Biology Program, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Proc Natl Acad Sci U S A 105:20055-62. 2008
    ....
  17. ncbi request reprint Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis
    Noah Fahlgren
    Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97330, USA
    Curr Biol 16:939-44. 2006
    ..In light of the functions of ARF3 and ARF4 in organ asymmetry, these data reveal multiple roles for TAS3 ta-siRNA-mediated regulation of ARF genes in developmental timing and patterning...
  18. ncbi request reprint Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana
    Edwards Allen
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Nat Genet 36:1282-90. 2004
    ..We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities...
  19. ncbi request reprint microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    Edwards Allen
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Cell 121:207-21. 2005
    ....
  20. pmc Genome-wide profiling and analysis of Arabidopsis siRNAs
    Kristin D Kasschau
    Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
    PLoS Biol 5:e57. 2007
    ..We conclude that the widespread accumulation patterns for RDR2- and DCL3-dependent siRNAs throughout the Arabidopsis genome largely reflect mechanisms to silence highly repeated sequences...
  21. pmc GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences
    Jason S Cumbie
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
    PLoS ONE 6:e25279. 2011
    ....
  22. pmc ASRP: the Arabidopsis Small RNA Project Database
    Adam M Gustafson
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
    Nucleic Acids Res 33:D637-40. 2005
    ..0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu...
  23. ncbi request reprint Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages
    Po Pu Liu
    Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
    Plant J 52:133-46. 2007
    ....
  24. pmc Expression of Arabidopsis MIRNA genes
    Zhixin Xie
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Physiol 138:2145-54. 2005
    ..The 5'-mapping data were combined with miRNA cloning and 3'-PCR data to definitively validate expression of at least 73 MIRNA genes. These data provide a molecular basis to explore regulatory mechanisms of miRNA expression in plants...
  25. pmc Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection
    Hernan Garcia-Ruiz
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
    Plant Cell 22:481-96. 2010
    ....
  26. pmc Splicing and dicing with a SERRATEd edge
    Taiowa A Montgomery
    Molecular and Cellular Biology Program, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Proc Natl Acad Sci U S A 105:8489-90. 2008
  27. pmc The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases
    Scott A Givan
    Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
    BMC Bioinformatics 8:479. 2007
    ..Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist...
  28. ncbi request reprint Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation
    Zhixin Xie
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
    Curr Biol 13:784-9. 2003
    ..These results indicate that DCL1 mRNA is subject to negative feedback regulation through the activity of a miRNA...
  29. ncbi request reprint Suppressor of RNA silencing encoded by Beet yellows virus
    Jonathan C Reed
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Virology 306:203-9. 2003
    ..Examination of the subcellular distribution in BYV-infected plants revealed that p21 is partitioned between soluble cytoplasmic form and proteinaceous inclusion bodies at the cell periphery...
  30. pmc Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs
    Noah Fahlgren
    Donald Danforth Plant Science Center, St Louis, Missouri, United States of America Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
    PLoS ONE 8:e77181. 2013
    ....
  31. pmc Virus-derived gene expression and RNA interference vector for grapevine
    Elizabeth G Kurth
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
    J Virol 86:6002-9. 2012
    ..The most significant applications of the viral vector include functional genomics of the grapevine and disease control via RNAi-enabled vaccination against pathogens or invertebrate pests...
  32. doi request reprint miRNA Target Prediction in Plants
    Noah Fahlgren
    Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
    Methods Mol Biol 592:51-7. 2010
    ..In plants, miRNA bind to target RNAs with a high degree of complementarity. In this chapter, a simple method for computationally predicting plant miRNA targets, using a position-dependent scoring system, is described...
  33. pmc Evolution and functional diversification of MIRNA genes
    Josh T Cuperus
    Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Cell 23:431-42. 2011
    ..The evolution of miRNA processing and functional diversity underscores the dynamic nature of miRNA-based regulation in complex regulatory networks...
  34. pmc Small RNAs and Arabidopsis. A fast forward look
    James C Carrington
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Physiol 138:565-6. 2005
  35. ncbi request reprint Loss-of-susceptibility mutants of Arabidopsis thaliana reveal an essential role for eIF(iso)4E during potyvirus infection
    Andrew D Lellis
    Center for Gene Research and Biotechnology and Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331, USA
    Curr Biol 12:1046-51. 2002
    ..eIF4E and eIF(iso)4E from different plant species were shown previously to interact with the genome-linked protein (VPg) of TEV and TuMV, respectively. Models to explain the roles of eIF(iso)4E during virus infection are presented...
  36. ncbi request reprint Genome streamlining in a cosmopolitan oceanic bacterium
    Stephen J Giovannoni
    Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
    Science 309:1242-5. 2005
    ..P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell...
  37. pmc Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex
    Kristina M Smith
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, 97331 7305, USA
    Eukaryot Cell 9:1549-56. 2010
    ..Our findings provide links between the key circadian activator and effectors in downstream regulatory pathways...
  38. pmc Endogenous and silencing-associated small RNAs in plants
    Cesar Llave
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
    Plant Cell 14:1605-19. 2002
    ..The accumulation of specific small RNAs was regulated developmentally. We propose that Arabidopsis small RNAs participate in a wide range of post-transcriptional and epigenetic events...
  39. ncbi request reprint Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319
    Javier F Palatnik
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Dev Cell 13:115-25. 2007
    ..Together, our findings reveal that functional specialization of miR159 and miR319 is achieved through both expression and sequence differences...
  40. ncbi request reprint Control of leaf morphogenesis by microRNAs
    Javier F Palatnik
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    Nature 425:257-63. 2003
    ..TCP genes with microRNA target sequences are found in a wide range of species, indicating that microRNA-mediated control of leaf morphogenesis is conserved in plants with very different leaf forms...
  41. ncbi request reprint Specialization and evolution of endogenous small RNA pathways
    Elisabeth J Chapman
    Department of Biology, Myers Hall, 915 East Third Street, Indiana University, Bloomington, Indiana 47405, USA
    Nat Rev Genet 8:884-96. 2007
    ..Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms...
  42. pmc A uniform system for microRNA annotation
    Victor Ambros
    Dartmouth Medical School Department of Genetics, Hanover, New Hampshire 03755, USA
    RNA 9:277-9. 2003
    ..Finally, an online clearinghouse for miRNA gene name assignments is provided by the Rfam database of RNA families...
  43. ncbi request reprint Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats
    Daniel Zilberman
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Curr Biol 14:1214-20. 2004
    ....
  44. ncbi request reprint Role of transposable elements in heterochromatin and epigenetic control
    Zachary Lippman
    Watson School of Biological Sciences and Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Nature 430:471-6. 2004
    ..This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs...
  45. ncbi request reprint The consequences of gene and genome duplication in plants
    Susan R Wessler
    Curr Opin Plant Biol 8:119-21. 2005
  46. pmc Identification and characterization of human cytomegalovirus-encoded microRNAs
    Finn Grey
    Department of Molecular Microbiology and Immunology, Oregon Health Sciences University, Portland, OR 97201, USA
    J Virol 79:12095-9. 2005
    ..These studies demonstrate that human cytomegalovirus encodes multiple conserved miRNAs and suggest that human cytomegalovirus may utilize an miRNA strategy to regulate cellular and viral gene function...
  47. ncbi request reprint Transgenically expressed viral RNA silencing suppressors interfere with microRNA methylation in Arabidopsis
    Bin Yu
    Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
    FEBS Lett 580:3117-20. 2006
    ..These findings suggest miRNA/miRNA* as the in vivo substrates for the HEN1 miRNA methyltransferase and raise intriguing possibilities regarding the cellular location of miRNA methylation...
  48. pmc Distinct expression patterns of natural antisense transcripts in Arabidopsis
    Stefan R Henz
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany
    Plant Physiol 144:1247-55. 2007
    ..Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process...
  49. pmc Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors
    Lóránt Lakatos
    Agricultural Biotechnology Center, Plant Biology Institute, Godollo, Hungary
    EMBO J 25:2768-80. 2006
    ..None of the suppressors affected the activity of preassembled RISC complexes. In contrast, each suppressor uniformly inhibited the siRNA-initiated RISC assembly pathway by preventing RNA silencing initiator complex formation...
  50. pmc PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans
    Pedro J Batista
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Cell 31:67-78. 2008
    ..Our findings demonstrate that 21U-RNAs are the piRNAs of C. elegans and link this class of small RNAs and their associated Piwi Argonaute to the maintenance of temperature-dependent fertility...