plant rna

Summary

Summary: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.

Top Publications

  1. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
  2. pmc Criteria for annotation of plant MicroRNAs
    Blake C Meyers
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Plant Cell 20:3186-90. 2008
  3. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
  4. ncbi Specific effects of microRNAs on the plant transcriptome
    Rebecca Schwab
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Dev Cell 8:517-27. 2005
  5. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
  6. ncbi 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
  7. pmc Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    Ramanjulu Sunkar
    Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Cell 16:2001-19. 2004
  8. ncbi Widespread translational inhibition by plant miRNAs and siRNAs
    Peter Brodersen
    Institut de Biologie Moleculaire des Plantes du CNRS, Unité Propre de Recherche 2357, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
    Science 320:1185-90. 2008
  9. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
  10. ncbi A plant miRNA contributes to antibacterial resistance by repressing auxin signaling
    Lionel Navarro
    Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
    Science 312:436-9. 2006

Research Grants

Detail Information

Publications307 found, 100 shown here

  1. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
    ..The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future...
  2. pmc Criteria for annotation of plant MicroRNAs
    Blake C Meyers
    Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Plant Cell 20:3186-90. 2008
    ..Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature...
  3. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
    ..The expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAs can be induced by environmental stress...
  4. ncbi Specific effects of microRNAs on the plant transcriptome
    Rebecca Schwab
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Dev Cell 8:517-27. 2005
    ..This finding unifies the view of plant miRNA action...
  5. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
    ..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants...
  6. ncbi 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...
  7. pmc Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    Ramanjulu Sunkar
    Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Cell 16:2001-19. 2004
    ....
  8. ncbi Widespread translational inhibition by plant miRNAs and siRNAs
    Peter Brodersen
    Institut de Biologie Moleculaire des Plantes du CNRS, Unité Propre de Recherche 2357, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
    Science 320:1185-90. 2008
    ..Also as in animals, the decapping component VARICOSE (VCS)/Ge-1 is required for translational repression by miRNAs, which suggests that the underlying mechanisms in the two kingdoms are related...
  9. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  10. ncbi A plant miRNA contributes to antibacterial resistance by repressing auxin signaling
    Lionel Navarro
    Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
    Science 312:436-9. 2006
    ..Repression of auxin signaling restricts P. syringae growth, implicating auxin in disease susceptibility and miRNA-mediated suppression of auxin signaling in resistance...
  11. ncbi 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
    ....
  12. ncbi A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development
    Xuemei Chen
    Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 303:2022-5. 2004
    ..Therefore, miRNA172 likely acts in cell-fate specification as a translational repressor of APETALA2 in Arabidopsis flower development...
  13. pmc Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide
    Shijun Mi
    National Institute of Biological Sciences, No 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
    Cell 133:116-27. 2008
    ..This suggests that specialization of AGO complexes might involve remodeling the 5' end-binding pocket to accept certain small RNA sequences, perhaps explaining the evolutionary drive for miRNAs to initiate with uridine...
  14. ncbi Conservation and divergence of plant microRNA genes
    Baohong Zhang
    The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
    Plant J 46:243-59. 2006
    ..Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years...
  15. pmc The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development
    Herve Vaucheret
    Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, INRA, 78026 Versailles Cedex, France
    Genes Dev 18:1187-97. 2004
    ....
  16. ncbi FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis
    Laurent Corbesier
    Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D 50829 Cologne, Germany
    Science 316:1030-3. 2007
    ..Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering...
  17. pmc Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    Ryan Lister
    Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 133:523-36. 2008
    ..Finally, strand-specific mRNA-seq revealed altered transcript abundance of hundreds of genes, transposons, and unannotated intergenic transcripts upon modification of the DNA methylation state...
  18. pmc A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    Ramya Rajagopalan
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 20:3407-25. 2006
    ....
  19. ncbi Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
    Marcelo A German
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Nat Biotechnol 26:941-6. 2008
    ..This versatile approach will affect the study of other aspects of RNA processing beyond miRNA-target RNA pairs...
  20. pmc An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development
    Karen E Reid
    Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
    BMC Plant Biol 6:27. 2006
    ..Few statistically validated reference genes have been reported in grapevine. Moreover, success in isolating high quality RNA from grapevine tissues is typically limiting due to low pH, and high polyphenolic and polysaccharide contents...
  21. ncbi Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress
    Nathalie Nicot
    Centre de Recherche Public Gabriel Lippmann, Environment and Biotechnologies Research Unit, 41 rue du Brill, L 4422 Belvaux, Luxembourg
    J Exp Bot 56:2907-14. 2005
    ..The relative quantification of the hsp20.2 gene varied according to the internal control and the number of internal controls used, thus highlighting the importance of the choice of internal controls in such experiments...
  22. 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...
  23. ncbi A toolkit for analysing large-scale plant small RNA datasets
    Simon Moxon
    School of Computing Sciences, School of Biological Sciences, University of East Anglia, Norwich NR47TJ, UK
    Bioinformatics 24:2252-3. 2008
    ..Here, we describe a suite of web-based tools for processing plant small RNA datasets. Our tools can be used to identify micro RNAs and their targets, compare expression levels in sRNA loci, and find putative trans-acting siRNA loci...
  24. ncbi The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats
    H Cao
    Department of Botany, Duke University, Durham, North Carolina 27708 1000, USA
    Cell 88:57-63. 1997
    ..syringae in the absence of SAR induction...
  25. ncbi Small RNAs as big players in plant abiotic stress responses and nutrient deprivation
    Ramanjulu Sunkar
    Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
    Trends Plant Sci 12:301-9. 2007
    ..Subsequent studies have demonstrated an important functional role for these small RNAs in abiotic stress responses. This review focuses on recent advances, with emphasis on integration of small RNAs in stress regulatory networks...
  26. pmc Highly specific gene silencing by artificial microRNAs in Arabidopsis
    Rebecca Schwab
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Plant Cell 18:1121-33. 2006
    ..The design principles for amiRNAs have been generalized and integrated into a Web-based tool (http://wmd.weigelworld.org)...
  27. pmc Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit
    E J Stockinger
    Department of Crop and Soil Sciences, Michigan State University, East Lansing 48824, USA
    Proc Natl Acad Sci U S A 94:1035-40. 1997
    ..We conclude that CBF1 can function as a transcriptional activator that binds to the C-repeat/DRE DNA regulatory element and, thus, is likely to have a role in cold- and dehydration-regulated gene expression in Arabidopsis...
  28. pmc A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
    Qian Hao Zhu
    CSIRO Plant Industry, Canberra, ACT 2601, Australia
    Genome Res 18:1456-65. 2008
    ..Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner...
  29. ncbi Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots
    J R McConnell
    Department of Genetics, University of Wisconsin Madison, 53706, USA
    Nature 411:709-13. 2001
    ..This change probably renders the protein constitutively active, implicating this domain as a central regulator of protein function and the PHB and PHV proteins as receptors for an adaxializing signal...
  30. pmc Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
    Simon Moxon
    School of Computing, University of East Anglia, Norwich NR4 7TJ, United Kingdom
    Genome Res 18:1602-9. 2008
    ..This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation...
  31. ncbi Activation tagging of the floral inducer FT
    I Kardailsky
    Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 286:1962-5. 1999
    ..Instead, it is similar to the sequence of TERMINAL FLOWER 1 (TFL1), an inhibitor of flowering that also shares sequence similarity with membrane-associated mammalian proteins...
  32. pmc miRU: an automated plant miRNA target prediction server
    Yuanji Zhang
    Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
    Nucleic Acids Res 33:W701-4. 2005
    ..The miRU web server is available at http://bioinfo3.noble.org/miRU.htm...
  33. pmc MicroRNAs in plants
    Brenda J Reinhart
    Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Genes Dev 16:1616-26. 2002
    ..The previously described roles of CARPEL FACTORY in the development of Arabidopsis embryos, leaves, and floral meristems suggest that the miRNAs could play regulatory roles in the development of plants as well as animals...
  34. ncbi Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis
    A Samach
    John Innes Centre, Norwich NR4 7UH, UK
    Science 288:1613-6. 2000
    ..The SOC1 and FT genes are also regulated by a second flowering-time pathway that acts independently of CO. Thus, early target genes of CO define common components of distinct flowering-time pathways...
  35. ncbi The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering
    R Schaffer
    John Innes Centre, Norwich, United Kingdom
    Cell 93:1219-29. 1998
    ..Thus, constant expression of LHY disrupts several distinct circadian rhythms in Arabidopsis, and LHY may be closely associated with the central oscillator of the circadian clock...
  36. ncbi MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    Oliver Thimm
    Max Planck Institute for Molecular Plant Physiology, Golm, Germany
    Plant J 37:914-39. 2004
    ....
  37. ncbi 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...
  38. ncbi RNA silencing in plants
    David Baulcombe
    The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
    Nature 431:356-63. 2004
    ..We are now in a good position to investigate the full extent of this functional diversity in genetic and epigenetic mechanisms of genome control...
  39. ncbi Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice
    Kenong Xu
    Department of Plant Pathology, University of California, Davis, California 95616, USA
    Nature 442:705-8. 2006
    ..Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers...
  40. ncbi Evolution of plant microRNAs and their targets
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    Trends Plant Sci 13:343-9. 2008
    ..These data have provided a coherent set of hypotheses explaining the birth, selection and death of miRNAs in land plants...
  41. pmc Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
    Ryan D Morin
    Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
    Genome Res 18:571-84. 2008
    ..Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/...
  42. ncbi Identification and characterization of new plant microRNAs using EST analysis
    Bao Hong Zhang
    The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
    Cell Res 15:336-60. 2005
    ..Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized...
  43. pmc Dual coding of siRNAs and miRNAs by plant transposable elements
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 0230, USA
    RNA 14:814-21. 2008
    ..The siRNA-to-miRNA evolutionary transition is representative of a number of other regulatory mechanisms that evolved to silence TEs and were later co-opted to serve as regulators of host gene expression...
  44. pmc MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region
    Allison C Mallory
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142 1479, USA
    EMBO J 23:3356-64. 2004
    ....
  45. ncbi Photoreceptor regulation of CONSTANS protein in photoperiodic flowering
    Federico Valverde
    Max Planck Institute for Plant Breeding, Carl von Linne Weg 10, D 50829 Cologne, Germany
    Science 303:1003-6. 2004
    ..This layer of regulation refines the circadian rhythm in CO messenger RNA and is central to the mechanism by which day length controls flowering...
  46. ncbi A two-hit trigger for siRNA biogenesis in plants
    Michael J Axtell
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
    Cell 127:565-77. 2006
    ..Therefore, two "hits,"--often, but not always, two cleavage events--constitute a conserved trigger for siRNA biogenesis, a finding with implications for recognition and silencing of aberrant RNA...
  47. ncbi Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells
    T Lotan
    Division of Biological Sciences, University of California, Davis 95616, USA
    Cell 93:1195-205. 1998
    ..Our results suggest that LEC1 is an important regulator of embryo development that activates the transcription of genes required for both embryo morphogenesis and cellular differentiation...
  48. ncbi CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis
    P Suárez-López
    John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
    Nature 410:1116-20. 2001
    ..In addition, the late flowering phenotype of such mutants is corrected by overexpressing CO. Thus, CO acts between the circadian clock and the control of flowering, suggesting mechanisms by which day length regulates flowering time...
  49. ncbi RNA polymerase IV directs silencing of endogenous DNA
    A J Herr
    Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK
    Science 308:118-20. 2005
    ..The existence of this distinct silencing polymerase may explain the paradoxical involvement of an RNA silencing pathway in maintenance of transcriptional silencing...
  50. ncbi 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...
  51. ncbi Plant microRNA: a small regulatory molecule with big impact
    Baohong Zhang
    The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, 79409 1163, USA
    Dev Biol 289:3-16. 2006
    ..miRNAs regulate the expression of many important genes; a majority of these genes are transcriptional factors...
  52. ncbi Computational identification of novel microRNAs and targets in Brassica napus
    Fu Liang Xie
    Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
    FEBS Lett 581:1464-74. 2007
    ..The program is allowed to be run on Windows Operation System platform. miRNAassist is freely available if required...
  53. pmc Regulation of phosphate homeostasis by MicroRNA in Arabidopsis
    Tzyy Jen Chiou
    Institute of BioAgricultural Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China
    Plant Cell 18:412-21. 2006
    ..These results provide evidence that miRNA controls Pi homeostasis by regulating the expression of a component of the proteolysis machinery in plants...
  54. ncbi Adaptation of photoperiodic control pathways produces short-day flowering in rice
    Ryosuke Hayama
    Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916 5 Takayama, Ikoma 630 0101, Japan
    Nature 422:719-22. 2003
    ....
  55. pmc Nuclear processing and export of microRNAs in Arabidopsis
    Mee Yeon Park
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Proc Natl Acad Sci U S A 102:3691-6. 2005
    ..These results demonstrate that HST and PSD do not share RNA cargos in nuclear export and strongly suggest that there are multiple nuclear export pathways for these small RNAs in Arabidopsis...
  56. ncbi Epigenetics and plant evolution
    Ryan A Rapp
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
    New Phytol 168:81-91. 2005
    ....
  57. ncbi Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog
    C Strayer
    Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037, USA
    Science 289:768-71. 2000
    ..TOC1 is itself circadianly regulated and participates in a feedback loop to control its own expression...
  58. pmc Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing
    Patrice Dunoyer
    Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France
    Plant Cell 16:1235-50. 2004
    ..Therefore, silencing suppressors are valuable probes of the complexity of RNA silencing...
  59. pmc Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family
    Robert S Allen
    School of Biochemistry and Molecular Biology, Australian National University, Canberra ACT 0200, Australia
    Proc Natl Acad Sci U S A 104:16371-6. 2007
    ..This prediction was confirmed; the pleiotropic developmental defects of mir159ab are suppressed through the combined mutations of MYB33 and MYB65, demonstrating the narrow and specific target range of miR159a and miR159b...
  60. ncbi Characterisation of a pine MYB that regulates lignification
    Astrid Patzlaff
    Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
    Plant J 36:743-54. 2003
    ..Taken together, these findings are consistent with the hypothesis that PtMYB4 is sufficient to induce lignification, and that it may play this role during wood formation in pine...
  61. ncbi Regulation of copper homeostasis by micro-RNA in Arabidopsis
    Hiroaki Yamasaki
    Graduate School of Agriculture, Kyushu University, 6 10 1 Hakozaki, Higashiku, Fukuoka 812 8581, Japan
    J Biol Chem 282:16369-78. 2007
    ..We propose that miR398 is a key factor in copper homeostasis in plants and regulates the stability of mRNAs of major copper proteins under copper-limited conditions...
  62. pmc Various spatiotemporal expression profiles of anther-expressed genes in rice
    Tokunori Hobo
    Bioscience and Biotechnology Center, Nagoya University, Furocho, Chikusa, Nagoya, 464 8601 Japan
    Plant Cell Physiol 49:1417-28. 2008
    ....
  63. pmc Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana
    Leonardo Alves
    Genome Research and RNA based Regulation, Faculty of Biology, Center for Biotechnology CeBiTec, Bielefeld University, D 33594 Bielefeld, Germany
    Nucleic Acids Res 37:4010-21. 2009
    ..Our results are in line with recent observations that the majority of miRNA targets are not transcription factors...
  64. pmc Identification of novel and candidate miRNAs in rice by high throughput sequencing
    Ramanjulu Sunkar
    Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
    BMC Plant Biol 8:25. 2008
    ..Deep sequencing of small RNA libraries is an effective approach to uncover rare and lineage- and/or species-specific microRNAs (miRNAs) in any organism...
  65. pmc The origin of the naked grains of maize
    Huai Wang
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    Nature 436:714-9. 2005
    ..Our results demonstrate that modest genetic changes in single genes can induce dramatic changes in phenotype during domestication and evolution...
  66. ncbi Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics
    Kaoru Urano
    Gene Discovery Research Group, RIKEN Plant Science Center, 3 1 1 Koyadai, Tsukuba, Ibaraki, Japan
    Plant J 57:1065-78. 2009
    ..This metabolomics analysis revealed new molecular mechanisms of dynamic metabolic networks in response to dehydration stress...
  67. pmc Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance
    Jean Benoit Morel
    Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France
    Plant Cell 14:629-39. 2002
    ..Finally, we show that hypomorphic ago1 mutants are hypersensitive to virus infection, confirming the hypothesis that in plants PTGS is a mechanism of defense against viruses...
  68. pmc microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems
    Joonki Kim
    Graduate School of Chemistry and Molecular Engineering, Seoul National University, Seoul 151 742, South Korea
    Plant J 42:84-94. 2005
    ..miR166-assisted ATHB15 repression is likely to be a conserved mechanism that regulates vascular development in all vascular plants...
  69. pmc SERRATE: a new player on the plant microRNA scene
    Dajana Lobbes
    Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
    EMBO Rep 7:1052-8. 2006
    ..We show that SE is a general regulator of miRNA levels affecting the processing of primary miRNA to miRNA...
  70. pmc An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal
    Frank Schwach
    Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
    Plant Physiol 138:1842-52. 2005
    ..According to this idea, the secondary siRNAs mediate RNA silencing as an immediate response that slows down the systemic spreading of the virus into the growing point and newly emerging leaves...
  71. ncbi Methylation as a crucial step in plant microRNA biogenesis
    Bin Yu
    Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 307:932-5. 2005
    ..Our studies uncover a new and crucial step in plant miRNA biogenesis and have profound implications in the function of miRNAs...
  72. pmc A biochemical framework for RNA silencing in plants
    Guiliang Tang
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 17:49-63. 2003
    ..Here, we extend biochemical analysis to plant RNA silencing...
  73. ncbi 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...
  74. ncbi Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress
    Catalina Arenas-Huertero
    Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Av Universidad 2001, Cuernavaca, Morelos, Mexico
    Plant Mol Biol 70:385-401. 2009
    ..vulgaris. We propose that the novel miRNAs present in common bean and other legumes, are involved in regulation of legume-specific processes including adaptation to diverse external cues...
  75. pmc Evolution of Arabidopsis thaliana microRNAs from random sequences
    Felipe Fenselau de Felippes
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    RNA 14:2455-9. 2008
    ..Subsequent stabilization through coevolution with initially fortuitous targets may lead to fixation of a small subset of these proto-miRNA genes...
  76. ncbi Evidence that miRNAs are different from other RNAs
    B H Zhang
    The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409 1163, USA
    Cell Mol Life Sci 63:246-54. 2006
    ..001). The MFEI for miRNAs was 0.97, significantly higher than tRNAs (0.64), rRNAs (0.59), or mRNAs (0.65). Our findings should facilitate the prediction and identification of new miRNAs using computational and experimental strategies...
  77. ncbi CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana
    Wonkeun Park
    Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Curr Biol 12:1484-95. 2002
    ....
  78. ncbi Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed
    Kazumi Nakabayashi
    Plant Science Center, RIKEN, Suehiro cho 1 7 22, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    Plant J 41:697-709. 2005
    ..Our analyses reveal that transcriptomes of Arabidopsis seed are characterized by multiple regulatory mechanisms: epigenetic chromatin structures, chromosomal locations (e.g. co-regulated gene clusters) and cis-acting elements...
  79. ncbi Target mimicry provides a new mechanism for regulation of microRNA activity
    José Manuel Franco-Zorrilla
    Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
    Nat Genet 39:1033-7. 2007
    ..We coin the term 'target mimicry' to define this mechanism of inhibition of miRNA activity. Target mimicry can be generalized beyond the control of Pi homeostasis, as demonstrated using artificial target mimics...
  80. ncbi Plant RNA editing
    Anne Laure Chateigner-Boutin
    Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, Australia
    RNA Biol 7:213-9. 2010
    ....
  81. pmc The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development
    Anthony A Millar
    Commonwealth Scientific and Industrial Research Organization, Division of Plant Industry, Canberra ACT 2601, Australia
    Plant Cell 17:705-21. 2005
    ....
  82. pmc Separated transcriptomes of male gametophyte and tapetum in rice: validity of a laser microdissection (LM) microarray
    Keita Suwabe
    Graduate School of Life Sciences, Tohoku University, Sendai, 980 8577 Japan
    Plant Cell Physiol 49:1407-16. 2008
    ..These results indicate that the 44K LM-microarray is a reliable tool to analyze the gene expression profiles of two important cell types in the anther, the microspore/pollen and tapetum...
  83. pmc MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis
    Salah E Abdel-Ghany
    Biology Department and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado 80523, USA
    J Biol Chem 283:15932-45. 2008
    ..We propose that this mechanism allows plants to save copper for the most essential functions during limited copper supply...
  84. pmc High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
    Gyorgy Szittya
    School of Biological Sciences, University of East Anglia, Norwich, UK
    BMC Genomics 9:593. 2008
    ..High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatula)...
  85. pmc Epigenetic natural variation in Arabidopsis thaliana
    Matthew W Vaughn
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS Biol 5:e174. 2007
    ..This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means...
  86. ncbi Elucidation of the small RNA component of the transcriptome
    Cheng Lu
    Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
    Science 309:1567-9. 2005
    ..Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs...
  87. ncbi The developmental role of microRNA in plants
    Catherine A Kidner
    Institute of Molecular Plant Sciences, Edinburgh University, EH9 3JR, UK
    Curr Opin Plant Biol 8:38-44. 2005
    ..Over the past year, the list of known miRNAs, confirmed targets and developmental effects has expanded, as has the realization that they are conserved during evolution and that small RNAs can play a direct role in cell-cell signaling...
  88. ncbi 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...
  89. pmc The Arabidopsis LOS5/ABA3 locus encodes a molybdenum cofactor sulfurase and modulates cold stress- and osmotic stress-responsive gene expression
    L Xiong
    Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
    Plant Cell 13:2063-83. 2001
    ..Our results show that LOS5/ABA3 is a key regulator of ABA biosynthesis, stress-responsive gene expression, and stress tolerance...
  90. ncbi In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90
    Taichiro Iki
    Division of Plant Sciences, National Institute of Agrobiological Sciences NIAS, 2 1 2 Kannondai Tsukuba, Ibaraki 305 8602, Japan
    Mol Cell 39:282-91. 2010
    ..Removal of the siRNA passenger strand required the ribonuclease activity of AGO1, while that of the miRNA star strand did not. Based on these results, the mechanism of plant RISC formation is discussed...
  91. pmc Analysis of gene expression in cotton fiber initials
    Earl W Taliercio
    USDA ARS, Raleigh, NC 27607, USA
    BMC Plant Biol 7:22. 2007
    ..Little is known about the developmental pathway causing fiber to differentiate from ovular epidermal cells even though limits on the number of cells that differentiate into fiber will limit yield...
  92. pmc Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution
    Isam Fattash
    Faculty of Biology, Institute of Biology II, Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
    BMC Plant Biol 7:13. 2007
    ..Thus, the analysis of an early-branching species provides a window into the early evolution of fundamental regulatory processes in plants...
  93. ncbi Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression
    Z Y Wang
    Department of Molecular, Cell, and Developmental Biology, UCLA, Los Angeles, California 90095 1606, USA
    Cell 93:1207-17. 1998
    ..Furthermore, the expression of both endogenous CCA1 and the related LHY gene was suppressed. Our results suggest that CCA1 is a part of a feedback loop that is closely associated with the circadian clock in Arabidopsis...
  94. pmc Suppression of the microRNA pathway by bacterial effector proteins
    Lionel Navarro
    Institut de Biologie Moleculaire des Plantes, CNRS UPR 2353 Université Louis Pasteur, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
    Science 321:964-7. 2008
    ..These results provide evidence that, like viruses, bacteria have evolved to suppress RNA silencing to cause disease...
  95. ncbi High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis)
    Deyou Qiu
    Department of Molecular Biology, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
    Gene 436:37-44. 2009
    ....
  96. ncbi MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome
    Ning Bao
    Program in Plant Breeding and Plant Genetics, University of Wisconsin, Madison, WI 53706, USA
    Dev Cell 7:653-62. 2004
    ..These results suggest a model in which the microRNA interacts with nascent, newly processed PHB mRNA to alter chromatin of the corresponding PHB template DNA predominantly in differentiated cells...
  97. pmc Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions
    Yukio Kurihara
    Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3 8 1, Meguro ku, Tokyo 153 8902, Japan
    Proc Natl Acad Sci U S A 101:12753-8. 2004
    ..Our result is direct evidence that DCL1 is involved in processing of pri- and pre-miRNA...
  98. ncbi Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock
    D Alabadi
    Department of Cell Biology and Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, CA 92037, USA
    Science 293:880-3. 2001
    ..Conversely, TOC1 appears to participate in the positive regulation of LHY and CCA1 expression. Our results indicate that these interactions form a loop critical for clock function in Arabidopsis...
  99. pmc The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis
    Iain Searle
    Max Planck Institute for Plant Breeding, D 50829 Cologne, Germany
    Genes Dev 20:898-912. 2006
    ..Thus vernalization relieves transcriptional repression of key regulatory genes in both the leaf and meristem, allowing production of systemic signals in the leaves and conferring competence on the meristem to respond to these signals...
  100. ncbi Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana
    Riki Kawaguchi
    Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521 0124, USA
    Plant J 38:823-39. 2004
    ..Thus, the abundance of PS mRNA may provide a more accurate estimate of gene expression than total cellular mRNA because of extensive differential translational regulation...
  101. pmc Identification and characterization of endogenous small interfering RNAs from rice
    Ramanjulu Sunkar
    Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, 2150 Batchelor Hall, University of California, Riverside, CA 92521, USA
    Nucleic Acids Res 33:4443-54. 2005
    ..Using RNA ligase-mediated-5' rapid amplification of cDNA end assays, we validated three of the predicted targets and provided evidence for both cis- and trans-silencing of target genes by siRNAs-guided mRNA cleavage...

Research Grants21

  1. tRNA mediated assembly in an icosahedral RNA virus
    A L Rao; Fiscal Year: 2006
    ..transcriptases while the tRNA-like structural elements (TLS) found at the 3' end of the genomes of many plant RNA viruses serve as efficient origins of replications...
  2. Zeiss LSM 510 META Confocal Microscope
    JAMES CARRINGTON; Fiscal Year: 2003
    ....
  3. ACTIVITY AND TRANSPORT OF TOBACCO ETCH VIRUS PROTEINASE
    JAMES CARRINGTON; Fiscal Year: 2003
    ..Identification of these host mutants will provide the starting point for isolation of genes involved in NIa-interacting reactions and pathways. ..
  4. GENETIC ANALYSIS OF RNA VIRUS-HOST INTERACTION
    JAMES CARRINGTON; Fiscal Year: 2007
    ..Interactions between several viral silencing suppressors and cellular complexes and regulatory RNAs, and the interactions between suppressors and microRNA-controlled developmental pathways, will be examined. ..
  5. Roles of host RNA binding proteins in virus replication
    Peter Nagy; Fiscal Year: 2008
    ..The tractable in vitro and in vivo TBSV system developed by the investigator could prove beneficial to studies of other, less amenable RNA viruses. [unreadable] [unreadable] [unreadable]..
  6. Genetics of DNA Methylation Patterning of Arabidopsis
    Steven Jacobsen; Fiscal Year: 2008
    ....
  7. 2007 Epigenetics Gordon Research Conference
    Steven Jacobsen; Fiscal Year: 2007
    ..Perhaps equally importantly, it will launch the careers of new scientists in this frontier area. [unreadable] [unreadable] [unreadable]..
  8. GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA
    Justin O Borevitz; Fiscal Year: 2010
    ..The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL. ..
  9. Trafficking, persistence and evolution of HIV in the CNS
    Peter Simmonds; Fiscal Year: 2005
    ....
  10. Dissecting the mechanism of viral RNA recombination
    Peter Nagy; Fiscal Year: 2004
    ..Knowledge of recombination promises untold health benefits by providing means to limit virus infections and safer vaccines. ..
  11. ANALYSIS OF A LIGHT-REGULATED DEVELOPMENT SWITCH
    Xing Wang Deng; Fiscal Year: 2003
    ..abstract_text> ..
  12. Understanding the Mechanism of RNA Interference (RNAi)
    Phillip Zamore; Fiscal Year: 2009
    ....
  13. Host factors involved in viral RNA recombination
    Peter Nagy; Fiscal Year: 2006
    ..Knowledge of recombination promises untold health benefits by providing means to limit virus infections and to develop safer vaccines. ..
  14. Identification of the ribosomal target of Shiga-like toxins
    NILGUN TUMER; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  15. REGULATION OF POST-TRANSCRIPTIONAL GENE SILENCING
    Vicki Vance; Fiscal Year: 2004
    ..Given the antiviral nature of gene silencing in plants, understanding PTGS in plants could well lead to the development of antiviral strategies in humans. ..
  16. Mechanism of action of ricin A chain
    NILGUN TUMER; Fiscal Year: 2005
    ..These studies will aid in the design of protection strategies against toxins that are classified as high-risk candidates for bioterrorism. ..
  17. Comparative Genomics in the Enterobateriaceae
    Sandra Clifton; Fiscal Year: 2009
    ....
  18. Expression of Human Therapeutic Proteins in Transgenic Tobacco Chloroplasts
    Henry Daniell; Fiscal Year: 2010
    ..Successful completion of these studies would make transgenic chloroplasts ideal bioreactors for the production of safe and less expensive therapeutic proteins and open the door for in depth studies of membrane proteins. ..
  19. Role of an essential RNA chaperone in virus replication
    Peter Nagy; Fiscal Year: 2006
    ....