plant gene expression regulation

Summary

Summary: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.

Top Publications

  1. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
  2. ncbi Reactive oxygen species: metabolism, oxidative stress, and signal transduction
    Klaus Apel
    Institute of Plant Sciences, Swiss Federal Institute of Technology, Universitätstr 2, 8092 Zurich, Switzerland
    Annu Rev Plant Biol 55:373-99. 2004
  3. 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
  4. ncbi 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
  5. 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
  6. ncbi Prediction of plant microRNA targets
    Matthew W Rhoades
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
    Cell 110:513-20. 2002
  7. ncbi Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant J 31:279-92. 2002
  8. pmc Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis
    Q Liu
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, Ministry of Agriculture, Forestry, and Fisheries, 2 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant Cell 10:1391-406. 1998
  9. ncbi MAP kinase signalling cascade in Arabidopsis innate immunity
    Tsuneaki Asai
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 415:977-83. 2002
  10. 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

Detail Information

Publications312 found, 100 shown here

  1. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
    ..This report summarizes the present status of this database and available tools...
  2. ncbi Reactive oxygen species: metabolism, oxidative stress, and signal transduction
    Klaus Apel
    Institute of Plant Sciences, Swiss Federal Institute of Technology, Universitätstr 2, 8092 Zurich, Switzerland
    Annu Rev Plant Biol 55:373-99. 2004
    ..Considering recent ROS-induced genome-wide expression analyses, the possible functions and mechanisms for ROS sensing and signaling in plants are compared with those in animals and yeast...
  3. 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...
  4. ncbi 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
    ....
  5. 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...
  6. ncbi Prediction of plant microRNA targets
    Matthew W Rhoades
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
    Cell 110:513-20. 2002
    ..The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages...
  7. ncbi Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant J 31:279-92. 2002
    ....
  8. pmc Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis
    Q Liu
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, Ministry of Agriculture, Forestry, and Fisheries, 2 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant Cell 10:1391-406. 1998
    ..These results indicate that two independent families of DREB proteins, DREB1 and DREB2, function as trans-acting factors in two separate signal transduction pathways under low-temperature and dehydration conditions, respectively...
  9. ncbi MAP kinase signalling cascade in Arabidopsis innate immunity
    Tsuneaki Asai
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 415:977-83. 2002
    ..Activation of this MAPK cascade confers resistance to both bacterial and fungal pathogens, suggesting that signalling events initiated by diverse pathogens converge into a conserved MAPK cascade...
  10. 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...
  11. 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
    ....
  12. ncbi Gene networks involved in drought stress response and tolerance
    Kazuo Shinozaki
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 203 0045 Japan
    J Exp Bot 58:221-7. 2007
    ..A description is also provided of how various genes involved in stress tolerance were applied in genetic engineering of dehydration stress tolerance in transgenic Arabidopsis plants...
  13. pmc PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
    ..New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/...
  14. ncbi Systemic acquired resistance
    W E Durrant
    Developmental, Cell, and Molecular Biology Group, Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Annu Rev Phytopathol 42:185-209. 2004
    ..We discuss the molecular and genetic data that have contributed to our understanding of SAR and present a model describing the sequence of events leading from initial infection to the induction of defense genes...
  15. 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...
  16. ncbi The JAZ family of repressors is the missing link in jasmonate signalling
    A Chini
    Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnologia CSIC, Campus Universidad Autonoma, 28049 Madrid, Spain
    Nature 448:666-71. 2007
    ..Furthermore, we demonstrate the existence of a regulatory feed-back loop involving MYC2 and JAZ proteins, which provides a mechanistic explanation for the pulsed response to jasmonate and the subsequent desensitization of the cell...
  17. ncbi Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006
    ....
  18. ncbi Regulators of PP2C phosphatase activity function as abscisic acid sensors
    Yue Ma
    Lehrstuhl fur Botanik, Technische Universitat Munchen, Am Hochanger 4, D 85354 Freising, Germany
    Science 324:1064-8. 2009
    ..Other RCARs also mediated ABA-dependent regulation of ABI1 and ABI2, consistent with a combinatorial assembly of receptor complexes...
  19. 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...
  20. ncbi bZIP transcription factors in Arabidopsis
    Marc Jakoby
    MPI for Plant Breeding Research, 50829, Koln, Germany
    Trends Plant Sci 7:106-11. 2002
    ..This integration is essential for a complete functional characterization of bZIP transcription factors in plants, and to identify functional redundancies among AtbZIP factors...
  21. 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...
  22. ncbi Origin, biogenesis, and activity of plant microRNAs
    Olivier Voinnet
    Institut de Biologie Moleculaire des Plantes, CNRS UPR2357 Université de Strasbourg, 67084 Strasbourg, France
    Cell 136:669-87. 2009
    ..This Review discusses current advances in our understanding of the origin, biogenesis, and mode of action of plant miRNAs and draws comparisons with their metazoan counterparts...
  23. pmc JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis
    Oscar Lorenzo
    Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Campus Universidad Autonoma, 28049 Madrid, Spain
    Plant Cell 16:1938-50. 2004
    ....
  24. 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...
  25. 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...
  26. ncbi Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis
    Jiri Friml
    Zentrum für Molekularbiologie der Pflanzen, Universitat Tubingen, Auf der Morgenstelle 3, 72076 Tubingen, Germany
    Nature 426:147-53. 2003
    ..Our results indicate how the establishment of cell polarity, polar auxin efflux and local auxin response result in apical-basal axis formation of the embryo, and thus determine the axiality of the adult plant...
  27. ncbi The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots
    Ikram Blilou
    Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
    Nature 433:39-44. 2005
    ..Our data reveal an interaction network of auxin transport facilitators and root fate determinants that control patterning and growth of the root primordium...
  28. ncbi Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR
    Mukesh Jain
    Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India
    Biochem Biophys Res Commun 345:646-51. 2006
    ..The expression of these genes (with more uniform expression) can be used for normalization of real-time PCR results for gene expression studies in a wide variety of samples in rice...
  29. ncbi The F-box protein TIR1 is an auxin receptor
    Nihal Dharmasiri
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Nature 435:441-5. 2005
    ..Finally, TIR1 synthesized in insect cells binds Aux/IAA proteins in an auxin-dependent manner. Together, these results indicate that TIR1 is an auxin receptor that mediates Aux/IAA degradation and auxin-regulated transcription...
  30. ncbi Isochorismate synthase is required to synthesize salicylic acid for plant defence
    M C Wildermuth
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 414:562-5. 2001
    ..Here we show, by cloning and characterizing an Arabidopsis defence-related gene (SID2) defined by mutation, that SA is synthesized from chorismate by means of ICS, and that SA made by this pathway is required for LAR and SAR responses...
  31. pmc Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway
    Sarah Fowler
    Department of Energy Plant Research Laboratory and Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824 1312, USA
    Plant Cell 14:1675-90. 2002
    ....
  32. ncbi Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis
    Sang Dong Yoo
    Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
    Nat Protoc 2:1565-72. 2007
    ..The cell system offers reliable guidelines for further comprehensive analysis of complex regulatory mechanisms in whole-plant physiology, immunity, growth and development...
  33. pmc ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis
    Viswanathan Chinnusamy
    Department of Plant Sciences, University of Arizona, Tucson 85721, USA
    Genes Dev 17:1043-54. 2003
    ..ICE1 is expressed constitutively, and its overexpression in wild-type plants enhances the expression of the CBF regulon in the cold and improves freezing tolerance of the transgenic plants...
  34. 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...
  35. pmc Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process
    Marino Expósito-Rodríguez
    Instituto de Productos Naturales y Agrobiología CSIC, Avda, Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain
    BMC Plant Biol 8:131. 2008
    ..In the present report we describe the first systematic evaluation of potential internal controls during tomato development process to identify which are the most reliable for transcript quantification by real-time RT-PCR...
  36. pmc Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice
    Honghong Hu
    National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Wuhan 430070, China
    Proc Natl Acad Sci U S A 103:12987-92. 2006
    ..DNA chip analysis revealed that a large number of stress-related genes were up-regulated in the SNAC1-overexpressing rice plants. Our data suggest that SNAC1 holds promising utility in improving drought and salinity tolerance in rice...
  37. ncbi Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation
    Cyril Zipfel
    Botanical Institute, Zurich Basel Plant Science Centre, University of Basel, Hebelstrasse 1, CH 4056 Basel, Switzerland
    Cell 125:749-60. 2006
    ..These results demonstrate that EFR is the EF-Tu receptor and that plant defense responses induced by PAMPs such as EF-Tu reduce transformation by Agrobacterium...
  38. ncbi Signals from chloroplasts converge to regulate nuclear gene expression
    Shai Koussevitzky
    Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 316:715-9. 2007
    ..We propose a model in which multiple indicators of aberrant plastid function in Arabidopsis are integrated upstream of GUN1 within plastids, which leads to ABI4-mediated repression of nuclear-encoded genes...
  39. pmc Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling
    Hiroshi Abe
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant Cell 15:63-78. 2003
    ..These results indicate that both AtMYC2 and AtMYB2 proteins function as transcriptional activators in ABA-inducible gene expression under drought stress in plants...
  40. ncbi Transcription factors in plant defense and stress responses
    Karam Singh
    CSIRO Plant Industry, Centre for Environmental and Life Sciences, Private Bag 5, Wembly WA 6913, Australia
    Curr Opin Plant Biol 5:430-6. 2002
    ..These studies have also revealed some of the complexity and overlap in the responses to different stresses, and are likely to lead to new ways to enhance crop tolerance to disease and environmental stress...
  41. ncbi Significance of inducible defense-related proteins in infected plants
    L C Van Loon
    Phytopathology, Institute of Environmental Biology, Science Faculty, Utrecht University, 3508 TB Utrecht, The Netherlands
    Annu Rev Phytopathol 44:135-62. 2006
    ....
  42. ncbi Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    Daniel Zilberman
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Nat Genet 39:61-9. 2007
    ..Our results indicate that genic transcription and DNA methylation are closely interwoven processes...
  43. pmc Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development
    C Wasternack
    Department of Natural Product Biotechnology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D 06120 Halle Saale, Germany
    Ann Bot 100:681-97. 2007
    ..Many of them alter gene expression positively or negatively in a regulatory network with synergistic and antagonistic effects in relation to other plant hormones such as salicylate, auxin, ethylene and abscisic acid...
  44. pmc Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses
    M Ashiq Rabbani
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant Physiol 133:1755-67. 2003
    ..Transcriptome analysis revealed novel stress-inducible genes, suggesting some differences between Arabidopsis and rice in their response to stress...
  45. pmc PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants
    Rajendra Bari
    Max Planck Institute for Molecular Plant Physiology, Science Park Golm, 14476 Potsdam, Germany
    Plant Physiol 141:988-99. 2006
    ....
  46. ncbi Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters
    Kazuko Yamaguchi-Shinozaki
    Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    Trends Plant Sci 10:88-94. 2005
    ....
  47. pmc Abscisic acid signaling in seeds and seedlings
    Ruth R Finkelstein
    Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
    Plant Cell 14:S15-45. 2002
  48. pmc Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance
    Ramanjulu Sunkar
    Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Cell 18:2051-65. 2006
    ..Thus, relieving miR398-guided suppression of CSD2 in transgenic plants is an effective new approach to improving plant productivity under oxidative stress conditions...
  49. ncbi Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways
    K Shinozaki
    Laboratory of Plant Molecular Biology, Tsukuba Life Science Center, Institute of Physical and Chemical Research RIKEN, Tsukuba, 305 0074, Japan
    Curr Opin Plant Biol 3:217-23. 2000
    ..Recent studies are providing evidence of differences between dehydration-signaling and cold-stress-signaling cascades, and of cross-talk between them...
  50. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
    ..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
  51. pmc Auxin: regulation, action, and interaction
    Andrew W Woodward
    Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
    Ann Bot 95:707-35. 2005
    ..The phytohormone auxin is critical for plant growth and orchestrates many developmental processes...
  52. 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
    ....
  53. pmc Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR
    Shin Young Hong
    Department of Chemistry, Seoul National University, Seoul, 151 742, Korea
    BMC Plant Biol 8:112. 2008
    ..Therefore, stable reference genes are necessary to normalize the gene expression data...
  54. pmc Glucosinolate metabolites required for an Arabidopsis innate immune response
    Nicole K Clay
    Department of Genetics, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
    Science 323:95-101. 2009
    ..Our study shows that well-studied plant metabolites, previously identified as important in avoiding damage by herbivores, are also required as a component of the plant defense response against microbial pathogens...
  55. ncbi Lignin biosynthesis
    Wout Boerjan
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Annu Rev Plant Biol 54:519-46. 2003
    ..In some cases, the potential value for agriculture of transgenic plants with modified lignin structure has been demonstrated. This review presents a current picture of monolignol biosynthesis, polymerization, and lignin structure...
  56. pmc Epigenetic reprogramming and small RNA silencing of transposable elements in pollen
    R Keith Slotkin
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Cell 136:461-72. 2009
    ..We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes...
  57. pmc Antagonistic interaction between abscisic acid and jasmonate-ethylene signaling pathways modulates defense gene expression and disease resistance in Arabidopsis
    Jonathan P Anderson
    Cooperative Research Centre for Tropical Plant Protection, University of Queensland, St Lucia, Queensland, 4072, Australia
    Plant Cell 16:3460-79. 2004
    ....
  58. ncbi OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression
    Joseph G Dubouzet
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 33:751-63. 2003
    ..OsDREB1A is potentially useful for producing transgenic monocots that are tolerant to drought, high-salt, and/or cold stresses...
  59. pmc Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression
    H Abe
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, Ibaraki, Japan
    Plant Cell 9:1859-68. 1997
    ..These results indicate that both the rd22BP1 (MYC) and ATMYB2 (MYB) proteins function as transcriptional activators in the dehydration- and ABA-inducible expression of the rd22 gene...
  60. 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...
  61. pmc ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
    ..With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis...
  62. pmc ABA is an essential signal for plant resistance to pathogens affecting JA biosynthesis and the activation of defenses in Arabidopsis
    Bruce A T Adie
    Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas, Campus Universidad Autonoma, 28049 Madrid, Spain
    Plant Cell 19:1665-81. 2007
    ..The results support a model for ABA affecting JA biosynthesis in the activation of defenses against this oomycete...
  63. pmc F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress
    Mukesh Jain
    Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India
    Plant Physiol 143:1467-83. 2007
    ..The structure and function of F-box proteins in plants is discussed in light of these results and the published information. These data will be useful for prioritization of F-box proteins for functional validation in rice...
  64. pmc Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    Shawn J Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
    Nature 452:215-9. 2008
    ....
  65. pmc Plant immunity requires conformational changes [corrected] of NPR1 via S-nitrosylation and thioredoxins
    Yasuomi Tada
    Department of Biology, Post Office Box 90338, Duke University, Durham, NC 27708, USA
    Science 321:952-6. 2008
    ..Thus, the regulation of NPR1 is through the opposing action of GSNO and TRX. These findings suggest a link between pathogen-triggered redox changes and gene regulation in plant immunity...
  66. ncbi Hd3a protein is a mobile flowering signal in rice
    Shojiro Tamaki
    Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916 5 Takayama, Ikoma 630 0101, Japan
    Science 316:1033-6. 2007
    ..We show that the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical meristem and induces flowering in rice. These results suggest that the Hd3a protein may be the rice florigen...
  67. ncbi ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination
    Jose L Reyes
    Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Plant J 49:592-606. 2007
    ..Our results suggest that ABA-induced accumulation of miR159 is a homeostatic mechanism to direct MYB33 and MYB101 transcript degradation to desensitize hormone signaling during seedling stress responses...
  68. pmc Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3
    Gang Wu
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Development 133:3539-47. 2006
    ..We conclude that vegetative phase change in Arabidopsis is regulated by an increase in the expression of SPL3 and probably also SPL4 and SPL5, and that this increase is a consequence of a decrease in the level of miR156...
  69. ncbi Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage
    Antony N Dodd
    Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
    Science 309:630-3. 2005
    ..This explains why plants gain advantage from circadian control...
  70. pmc ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense
    Oscar Lorenzo
    Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas, Campus Universidad Autonoma, 28049 Madrid, Spain
    Plant Cell 15:165-78. 2003
    ....
  71. pmc Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis
    Claire Lurin
    Unite de Recherche en Genomique Vegetale, Institut National de la Recherche Agronomique Centre National de la Recherche Scientifique Université d Evry Val d Essone, CP 5708, 91057 Evry Cedex, France
    Plant Cell 16:2089-103. 2004
    ..These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms...
  72. ncbi Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice
    Kazuo Nakashima
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 51:617-30. 2007
    ..We conclude that OsNAC6 may serve as a useful biotechnological tool for the improvement of stress tolerance in various kinds of plants...
  73. ncbi Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis
    Jonathan T Vogel
    Michigan State University Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 1312, USA
    Plant J 41:195-211. 2005
    ..In addition, ZAT12 downregulated the expression of the CBF genes indicating a role for ZAT12 in a negative regulatory circuit that dampens expression of the CBF cold response pathway...
  74. 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...
  75. pmc Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
    Blake C Meyers
    Department of Vegetable Crops, University of California, Davis, California 95616, USA
    Plant Cell 15:809-34. 2003
    ..The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges...
  76. pmc MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development
    Hui Shan Guo
    Laboratory of Molecular Cell Biology, Temasek Life Science Laboratory, National University of Singapore, 117604 Singapore
    Plant Cell 17:1376-86. 2005
    ..Moreover, the cleavage-resistant form of NAC1 mRNA was unaffected by auxin treatment. Our results indicate that auxin induction of miR164 provides a homeostatic mechanism to clear NAC1 mRNA to downregulate auxin signals...
  77. ncbi The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family
    Chen Yanhui
    Peking Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, National Key Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, 100871, Beijing, People s Republic of China
    Plant Mol Biol 60:107-24. 2006
    ..Our comprehensive analysis of this largest transcription factor superfamily of Arabidopsis and rice may help elucidate the possible biological roles of the MYB genes in various aspects of flowering plants...
  78. ncbi Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction
    Miin Feng Wu
    University of North Carolina at Chapel Hill, Department of Biology, CB 3280, Coker Hall, Chapel Hill, NC 27599 3280, USA
    Development 133:4211-8. 2006
    ..The essential patterning function of miR167 contrasts with cases from animals in which miRNAs reinforce or maintain transcriptionally established gene expression patterns...
  79. ncbi Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes
    Zhonglin Mou
    Developmental, Cell, and Molecular Biology Group, Department of Biology, P O Box 91000, Duke University, Durham, NC 27708, USA
    Cell 113:935-44. 2003
    ..These data provide a missing link between accumulation of SA and activation of NPR1 in the SAR signaling pathway...
  80. ncbi A high-resolution root spatiotemporal map reveals dominant expression patterns
    Siobhan M Brady
    Department of Biology, Duke University, Durham, NC 27708, USA
    Science 318:801-6. 2007
    ..Methods that combine these profiles demonstrate transcriptionally rich and complex programs that define Arabidopsis root development in both space and time...
  81. ncbi FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex
    Mitsutomo Abe
    Department of Botany, Graduate School of Science, Kyoto University, Sakyo ku, Kyoto 606 8502, Japan
    Science 309:1052-6. 2005
    ..FT may represent a long-distance signal in flowering...
  82. ncbi The wheat VRN2 gene is a flowering repressor down-regulated by vernalization
    Liuling Yan
    Department of Agronomy and Range Science, University of California, Davis, CA 95616, USA
    Science 303:1640-4. 2004
    ..Reduction of the RNA level of VRN2 by RNA interference accelerated the flowering time of transgenic winter-wheat plants by more than a month...
  83. ncbi Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation
    Michael Walter
    Institut fur Botanik und Botanischer Garten, Molekulare Entwicklungsbiologie der Pflanzen, Universitat Munster, Schlossplatz 4, 48149 Munster, Germany
    Plant J 40:428-38. 2004
    ..Consequently, the BiFC approach should significantly facilitate the visualization of the subcellular sites of protein interactions under conditions that closely reflect the normal physiological environment...
  84. pmc The tomato homolog of CORONATINE-INSENSITIVE1 is required for the maternal control of seed maturation, jasmonate-signaled defense responses, and glandular trichome development
    Lei Li
    Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
    Plant Cell 16:126-43. 2004
    ..These findings indicate that the JA/COI1 signaling pathway regulates distinct developmental processes in different plants and suggest a role for JA in the promotion of glandular trichome-based defenses...
  85. pmc Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype
    Robert T Gaeta
    Department of Agronomy, University of Wisconsin, Madison, Wisconsin, USA
    Plant Cell 19:3403-17. 2007
    ..Our data indicate that exchanges among homoeologous chromosomes are a major mechanism creating novel allele combinations and phenotypic variation in newly formed B. napus polyploids...
  86. ncbi Auxin regulates SCF(TIR1)-dependent degradation of AUX/IAA proteins
    W M Gray
    The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
    Nature 414:271-6. 2001
    ..Because domain II is conserved in nearly all AUX/IAA proteins in Arabidopsis, we propose that auxin promotes the degradation of this large family of transcriptional regulators, leading to diverse downstream effects...
  87. 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
    ....
  88. pmc The Arabidopsis CORONATINE INSENSITIVE1 protein is a jasmonate receptor
    Jianbin Yan
    Department of Biological Sciences, Tsinghua University, Beijing 100084, China
    Plant Cell 21:2220-36. 2009
    ..Taken together, these results demonstrate that COI1 directly binds to JA-Ile and COR and serves as a receptor for jasmonate...
  89. ncbi Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis
    Sona Pandey
    Biology Department, 208 Mueller Laboratory, Penn State University, University Park, PA 16802, USA
    Cell 136:136-48. 2009
    ..We propose that GTG proteins function both as a new type of G protein and as a class of membrane-localized ABA receptors...
  90. pmc MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis
    Bikram Datt Pant
    Max Planck Institute for Molecular Plant Physiology, Science Park Golm, Am Muhlenberg 1, 14476 Potsdam, Germany
    Plant J 53:731-8. 2008
    ..Hence the transported miR399 molecules retain biological activity. This is a demonstration of systemic control of a biological process, i.e. maintenance of plant Pi homeostasis, by a phloem-mobile microRNA...
  91. ncbi Auxin response factors
    Tom J Guilfoyle
    University of Missouri, Department of Biochemistry, 117 Schweitzer Hall, Columbia, MI 65211, USA
    Curr Opin Plant Biol 10:453-60. 2007
    ..Recent advances have provided information on regulation of ARF gene expression, ARF roles in growth and developmental processes, and target genes regulated by ARFs...
  92. pmc Common functions for diverse small RNAs of land plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:1750-69. 2007
    ..Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants...
  93. pmc Evolution of Arabidopsis MIR genes generates novel microRNA classes
    Franck Vazquez
    Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Maulbeerstrasse 66, 4058 Basel, Switzerland
    Nucleic Acids Res 36:6429-38. 2008
    ..Our results suggest that evolution of MIR genes is associated with gradual, overlapping changes in DCL usage resulting in specific size classes of miRNAs...
  94. pmc Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
    Klaas Vandepoele
    Department of Plant Systems Biology, Flanders Institute for Biotechnology, B 9052 Ghent, Belgium
    Plant Physiol 150:535-46. 2009
    ....
  95. 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
    ....
  96. pmc RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice
    Tae Ho Lee
    Division of Bioscience and Bioinformatics, Myong Ji University, Yongin, Kyonggido 449 728, Korea
    Plant Physiol 151:16-33. 2009
    ..The RAN database can be used as a tool to gain insight into a particular gene by examining its coexpression partners...
  97. pmc BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses
    Jun Xian He
    Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA
    Science 307:1634-8. 2005
    ....
  98. pmc Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development
    Michael J Prigge
    Department of Molecular, Cellular and Developmental Biology, University of Michigan, An Arbor, Michigan 48109 1048, USA
    Plant Cell 17:61-76. 2005
    ..Differences in expression patterns explain some of these genetic interactions, whereas other interactions are likely attributable to differences in protein function as indicated by cross-complementation studies...
  99. pmc Extensive demethylation of repetitive elements during seed development underlies gene imprinting
    Mary Gehring
    Howard Hughes Medical Institute HHMI, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Science 324:1447-51. 2009
    ..These data suggest that imprinting in plants evolved from targeted methylation of transposable element insertions near genic regulatory elements followed by positive selection when the resulting expression change was advantageous...
  100. pmc Repression of FLOWERING LOCUS C and FLOWERING LOCUS T by the Arabidopsis Polycomb repressive complex 2 components
    Danhua Jiang
    Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
    PLoS ONE 3:e3404. 2008
    ..Given the central roles of FLC and FT in flowering-time regulation in Arabidopsis, these findings suggest that the CLF-containing PRC2-like complexes play a significant role in control of flowering in Arabidopsis...
  101. ncbi The Mg-chelatase H subunit is an abscisic acid receptor
    Yuan Yue Shen
    China State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, 100094 Beijing, China
    Nature 443:823-6. 2006
    ..We show also that ABAR/CHLH is a ubiquitous protein expressed in both green and non-green tissues, indicating that it might be able to perceive the ABA signal at the whole-plant level...

Research Grants6

  1. Molecular Mechanisms of Genome Duplication
    ZENGJIAN CHEN; Fiscal Year: 2009
    ..abstract_text> ..
  2. Vernalization a cold-induced regulatory network establishing cellular memory
    Richard M Amasino; Fiscal Year: 2010
    ..A general understanding of epigenetic regulation in a range of multi-cellular organisms should ultimately contribute to the development of strategies to treat disease states. ..
  3. MEMBRANE FUNCTION IN MUTANTS OF CAENORHABDITIS ELEGANS
    John Browse; Fiscal Year: 2004
    ..Quantitative measures of low-temperature performance and thermotolerance of the range of desaturase mutants will be correlated with fatty acid composition and measurements of membrane fluidity. ..
  4. The role of chromatin remodeling in development
    Doris Wagner; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  5. Genetic analysis of a developmental clock in Arabidopsis thaliana
    RICHARD POETHIG; Fiscal Year: 2008
    ..These experiments will yield the first detailed picture of the molecular mechanism of vegetative phase change and provide significant new information about the regulation and function of small RNAs in plants. ..