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Genomes and Genes | James C CarringtonSummaryAffiliation: Oregon State University Country: USA Publications
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Publications
Role of microRNAs in plant and animal developmentJames 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...
Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targetingMiya 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...- Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in ArabidopsisJosh 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... 
Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formationTaiowa 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...- Update of ASRP: the Arabidopsis Small RNA Project databaseTyler 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/... - MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thalianaNoah 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... - High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genesNoah 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... - Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate stepElisabeth 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... - Diverse suppressors of RNA silencing enhance agroinfection by a viral repliconMarin 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... - Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencingJosh 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.... - Computational and analytical framework for small RNA profiling by high-throughput sequencingNoah 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... - P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unctionKristin 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... - Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNACesar 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.... - Genetic and functional diversification of small RNA pathways in plantsZhixin 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... - DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thalianaZhixin 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... - AGO1-miR173 complex initiates phased siRNA formation in plantsTaiowa 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.... - Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thalianaEdwards 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... - Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in ArabidopsisNoah 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... - microRNA-directed phasing during trans-acting siRNA biogenesis in plantsEdwards Allen
Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
Cell 121:207-21. 2005.... - Genome-wide profiling and analysis of Arabidopsis siRNAsKristin 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... - GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differencesJason S Cumbie
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
PLoS ONE 6:e25279. 2011.... - ASRP: the Arabidopsis Small RNA Project DatabaseAdam 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... - Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stagesPo Pu Liu
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
Plant J 52:133-46. 2007.... - Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infectionHernan 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.... - Expression of Arabidopsis MIRNA genesZhixin 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... - The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databasesScott 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... - Splicing and dicing with a SERRATEd edgeTaiowa 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 - Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradationZhixin 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... - Suppressor of RNA silencing encoded by Beet yellows virusJonathan 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... - Virus-derived gene expression and RNA interference vector for grapevineElizabeth 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... - Evolution and functional diversification of MIRNA genesJosh 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... - miRNA Target Prediction in PlantsNoah 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... - Small RNAs and Arabidopsis. A fast forward lookJames C Carrington
Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
Plant Physiol 138:565-6. 2005 - Genome streamlining in a cosmopolitan oceanic bacteriumStephen 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... - Loss-of-susceptibility mutants of Arabidopsis thaliana reveal an essential role for eIF(iso)4E during potyvirus infectionAndrew 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... - Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complexKristina 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... - Endogenous and silencing-associated small RNAs in plantsCesar 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... - Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319Javier 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... - Control of leaf morphogenesis by microRNAsJavier F Palatnik
Department of Molecular Biology, Max Planck Institute for Developmental Biology, , 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... - A uniform system for microRNA annotationVictor 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... - Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeatsDaniel Zilberman
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
Curr Biol 14:1214-20. 2004.... - PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegansPedro 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... - Role of transposable elements in heterochromatin and epigenetic controlZachary 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... - The consequences of gene and genome duplication in plantsSusan R Wessler
Curr Opin Plant Biol 8:119-21. 2005 - Specialization and evolution of endogenous small RNA pathwaysElisabeth 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... - Identification and characterization of human cytomegalovirus-encoded microRNAsFinn 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... - Distinct expression patterns of natural antisense transcripts in ArabidopsisStefan 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... - Transgenically expressed viral RNA silencing suppressors interfere with microRNA methylation in ArabidopsisBin 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... - Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressorsLóránt 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...