Skip to main content
Article thumbnail
Location of Repository

Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants

By Debra J Skinner and Charles S Gasser
Topics: Research Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2664812
Provided by: PubMed Central

Suggested articles

Citations

  1. (2003). A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiology
  2. (1994). A seed shape mutant of Arabidopsis that is affected in integument development. Plant Cell
  3. (2000). A: AINTEGUMENTA promotes petal identity and acts as a negative regulator of AGAMOUS. Plant Cell
  4. (2003). AF: Assumptionfree analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett
  5. (2006). AINTEGUMENTA contributes to organ polarity and regulates growth of lateral organs in combination with YABBY genes. Plant Physiology
  6. (2004). Arabidopsis microarray database and analysis toolbox. Plant Physiol
  7. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol
  8. (2003). C: The identification of candidate genes for a reverse genetic analysis of development and function in the Arabidopsis gynoecium. Plant Physiol
  9. (1991). Callose as an indicator of sterile ovules. Phytomorphology
  10. (2004). CD: Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.
  11. (2005). CJ: Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis. Plant Cell
  12. (2006). CS: ABERRANT TESTA SHAPE encodes a KANADI family member, linking polarity determination to separation and growth of Arabidopsis ovule integuments. Plant J
  13. (1998). CS: Arabidopsis TSO1 regulates directional processes in cells during floral organogenesis. Genetics
  14. (1999). CS: INNER NO OUTER regulates abaxial-adaxial patterning in Arabidopsis ovules. Genes Dev
  15. (1997). CS: Interactions among genes regulating ovule development in Arabidopsis thaliana. Genetics
  16. (2005). CS: Mechanisms of Derived Unitegmy among Impatiens Species. Plant Cell
  17. (1992). CS: Ovule development in wild-type Arabidopsis and two female-sterile mutants. Plant Cell
  18. (2004). CS: Regulation of ovule development. Plant Cell
  19. (2002). CS: SUPERMAN attenuates positive INNER NO OUTER autoregulation to maintain polar development of Arabidopsis ovule outer integuments. Development
  20. (1994). CS: The Arabidopsis floral homeotic gene BELL (BEL1) controls ovule development through negative regulation of AGAMOUS gene (AG). Proc Natl Acad Sci USA
  21. (2001). CS: The Arabidopsis HUELLENLOS gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein. Plant Cell
  22. (1995). CS: The Arabidopsis SUPERMAN gene mediates asymmetric growth of the outer integument of ovules. Plant Cell
  23. (2002). De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol
  24. (1996). DR: AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth. Plant Cell
  25. (2001). DR: SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein. Development
  26. (1987). Duplication of CaMV 35S promoter sequences creates a strong enhancer for plant genes. Science
  27. (2000). E: Monitoring genome-wide expression in plants. Curr Opin Biotechnol
  28. (2000). E: Regulation of SUP expression identifies multiple regulators involved in Arabidopsis floral meristem development. Plant Cell
  29. (1990). Early flower development in Arabidopsis. Plant Cell
  30. (1999). Ectopic expression of AINTEGUMENTA in Arabidopsis plants results in increased growth of floral organs. Dev Genet
  31. (2004). EM: Floral induction in tissue culture: a system for the analysis of LEAFY-dependent gene regulation. Plant J
  32. (2003). EM: Whorl-specific expression of the SUPERMAN gene of Arabidopsis is mediated by cis elements in the transcribed region. Curr Biol
  33. (2003). Empirical analysis of transcriptional activity in the Arabidopsis genome. Science
  34. (2005). Environmental stress alters genes expression and induces ovule abortion: reactive oxygen species appear as ovules commit to abort. Planta
  35. (2006). Eshed Y: Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in fiverse species. Plant Cell
  36. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology
  37. (1994). FA: The BTB domain, found primarily in zinc finger proteins, defines an evolutionarily conserved family that includes several developmentally regulated genes in Drosophila.
  38. (2003). FCH: Dissecting plant meiosis using Arabidopsis thaliana mutants.
  39. (2000). Fischer RL: Plant organ size control: AINTEGUMENTA regulates growth and cell numbers during organogenesis.
  40. (2005). Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell
  41. (1998). Genetic analysis of ovule development. Ann Rev Plant Physiol Plant Mol Biol
  42. (2007). Genetic and molecular interactions between BELL1 and MADS box factors support ovule development in Arabidopsis. Plant Cell
  43. (2006). Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell
  44. (2004). Genome-wide analysis of spatial gene expression in Arabidopsis flowers. Plant Cell
  45. (2004). Genomic identification of direct target genes of LEAFY. Proc Natl Acad Sci USA
  46. (2007). Grossniklaus U: Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte. Genome Biology
  47. (2003). Grossniklaus U: The Polycomb -group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev
  48. (2000). GW: Differentiation of mucilage secretory cells of the Arabidopsis seed coat. Plant Physiol
  49. (1994). GW: Homeotic transformation of ovules into carpel-like structures in Arabidopsis. Plant Cell
  50. (1987). Handling of Arabidopsis. In Arabidopsis Information Service, v 24: Genetic Resources in Arabidopsis Edited by: Kranz AR. Frankfurt, Germany: Arabidopsis Information Service;
  51. (2004). Hauser BA: Ovule abortion in Arabidopsis triggered by stress. Plant Physiol
  52. (1996). Hoge JH: Novel members of a family of AT hook-containing DNA-binding proteins from rice are identified through their in vitro interaction with consensus target sites of plant and animal homeodomain proteins. Plant Mol Biol
  53. (2004). Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol Biol
  54. (2008). Integrating molecular phylogenetic and paloebotanical evidence on origin of the flower.
  55. (2004). Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol
  56. (2000). Involvement of CUPSHAPED COTYLEDON genes in gynoecium and ovule development in Arabidopsis thaliana. Plant Cell Physiol
  57. (2003). Irish VF: Global identification of target genes regulated by APETALA3 and PISTILLATA floral homeotic gene action. Plant Cell
  58. (2003). Isolation, sequence analysis, and expression studies of florally expressed cDNAs in Arabidopsis. Plant Mol Biol
  59. (2006). JC: RABBIT EARS is a secondwhorl repressor of AGAMOUS that maintains spatial boundaries in Arabidopsis flowers.
  60. (2001). JL: Establishment of polarity in lateral organs of plants. Curr Biol
  61. (2003). JL: Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr Biol
  62. (2004). JW: Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol
  63. (2000). Klink VP: Regulation of gynoecium marginal tissue formation by LEUNIG and AINTEGUMENTA. Plant Cell
  64. (2005). Krizek BA: AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or division-competent states. Plant Mol Biol
  65. L: MADS-box protein complexes control carpel and ovule development in Arabidopsis. Plant Cell 2003, 15:2603-2611.BMC Plant Biology 2009, 9:29 http://www.biomedcentral.com/1471-2229/9/29 Page 19 of 20 (page number not for citation purposes)
  66. (2007). L: REM18 and REM53: two direct targets of the ovule identity complex of Arabidopsis.
  67. (1998). Landsman D: AT-hook motifs identified in a wide variety of DNA-binding proteins.
  68. (2004). Laux T: Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development
  69. (2005). Leyser O: The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature
  70. (2003). Limma: Linear Models for Microarray Data User's Guide.
  71. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
  72. (2003). Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell
  73. (2000). Lolle SJ: FIDDLEHEAD, a gene required to suppress epidermal cell interactions in Arabidopsis, encodes a putative lipid biosynthetic enzyme. Proc Natl Acad Sci USA
  74. (2002). Martinez-Zapater JM: AtREM1, a member of a new family of B3 domain-containing genes, is preferentially expressed in reproductive meristems. Plant Physiol
  75. (2000). Meshi T: AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell
  76. (2003). MF: Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature
  77. (2000). MF: B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature
  78. (2006). MF: NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis. Development
  79. (2000). MF: Redundant regulation of meristem identity and plant architecture by FRUITFULL,
  80. (2000). MF: SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature
  81. (2004). Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. Plant Cell
  82. (1999). Molecular genetics of gynoecium development in Arabidopsis. Curr Top Dev Biol
  83. (2005). Nasrallah JB: Genome-wide identification of genes expressed in Arabidopsis pistils specifically along the path of pollen tube growth. Plant Physiol
  84. (2004). Okada K: RABBIT EARS, encoding a SUPERMAN-like zinc finger protein, regulates petal development in Arabidopsis thaliana. Development
  85. (2005). Plant development is regulated by a family of auxin receptor F box proteins. Dev Cell
  86. (2003). Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell
  87. (2004). Poovaiah BW: A novel family of Ca2+/calmodulin-binding proteins involved in transcriptional regulation: interaction with fsh/Ring3 class transcription activators. Plant Mol Biol
  88. (2002). Post-analysis follow-up and validation of microarray experiments.
  89. (2008). Raikhel NV: Trehalose-6-Phosphate Synthase/Phosphatase Regulates Cell Shape and Plant Architecture in Arabidopsis. Plant Physiol
  90. (2003). Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis. Development
  91. (2008). RG: SEUSS and AINTEGUMENTA mediate patterning and ovule initiation during gynoecium medial domain development. Plant Physiol
  92. (1996). RL: The AINTEGUMENTA gene of Arabidopsis required for ovule and female gametophyte development is related to the floral homeotic gene APETALA2. Plant Cell
  93. (1995). RL: The BELL1 gene encodes a homeodomain protein involved in pattern formation in the Arabidopsis ovule primordium. Cell
  94. (1993). Robinson-Beers K: Pistil Development. Plant Cell
  95. (1995). Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries. Nature
  96. (2005). S: The transcriptome of Populus in elevated CO2. New Phytol
  97. (2001). Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods
  98. (1999). Schneitz K: Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana. Proc Natl Acad Sci USA
  99. (2004). Schneitz K: Pattern formation during early ovule development in Arabidopsis thaliana. Dev Biol
  100. (1996). SD: Identification of a meristem L1 layer-specific gene in Arabidopsis that is expressed during embryonic pattern formation and defines a new class of homeobox genes. Plant Cell
  101. (2005). Shinozaki K: RARTF: Database and tools for complete sets of Arabidopsis transcription factors.
  102. (1996). SJ: ZZ and TAZ: new putative zinc fingers in dystrophin and other proteins. Trends Biochem Sci
  103. (2004). Smyth GK: limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics
  104. (2005). Soderman E: Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiol
  105. (2002). Speed T: Replicated microarray data. Stat Sinica
  106. (2003). Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics
  107. (1999). Sundaresan V: Analysis of flanking sequences from Dissociation insertion lines: A database for reverse genetics in Arabidopsis. Plant Cell
  108. (1999). Sundaresan V: The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein. Genes Dev
  109. (2002). T: WUSCHEL signaling functions in interregional communication during Arabidopsis ovule development. Genes Dev
  110. (2007). TD: Regulation of telomerase in Arabidopsis by BT2, an apparent target of TELOMERASE ACTIVATOR1. Plant Cell
  111. (1993). The amino acid sequence of Ole e I, the major allergen from olive tree (Olea europaea) pollen.
  112. (1999). The Arabidopsis det3 mutant reveals a central role for the vacuolar H(+)-ATPase in plant growth and development. Genes Dev
  113. (2004). The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence. Plant Physiol
  114. (1998). The ARF family of transcription factors and their role in plant hormone-responsive transcription. Cell Mol Life Sci
  115. (2005). The F-box protein TIR1 is an auxin receptor. Nature
  116. (2006). The LEAFY target LMI1 is a meristem identity regulator and acts together with LEAFY to regulate expression of CAULIFLOWER. Development
  117. (1999). The PERIANTHIA gene encodes a bZIP protein involved in the determination of floral organ number in Arabidopsis thaliana. Genes Dev
  118. (2005). The PRETTY FEW SEEDS2 gene encodes an Arabidopsis homeodomain protein that regulates ovule development. Development
  119. (2003). Tibshirani R: Statistical significance for genomewide studies.
  120. (2004). Tindell LD: Arabidopsis MPSS. An online resource for quantitative expression analysis. Plant Physiol
  121. (1999). TJ: Activation and repression of transcription by auxin-response factors.
  122. (2004). Torii KU: Synergistic interaction of three ERECTA-family receptor-like kinases controls Arabidopsis organ growth and flower development by promoting cell proliferation. Development
  123. (2003). TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics
  124. (1999). TR: Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA
  125. Transcriptional Regulation: a Genomics Overview. In The Arabidopsis Book (TAB)
  126. (1994). Treisman R: The POZ domain: a conserved protein-protein interaction motif. Genes Dev
  127. (2003). Twell D: Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol
  128. (2004). Twell D: Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol
  129. (2004). Udvardi MK: Realtime RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel rootand shoot-specific genes. Plant J
  130. (1998). VF: Discrete spatial and temporal cis-acting elements regulate transcription of the Arabidopsis floral homeotic gene APETALA3. Development
  131. (2000). von Heijne G: Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
  132. (1995). Wild-type ovule development in Arabidopsis thaliana: a light microscope study of cleared whole-mount tissue.
  133. (2007). Y: AGF1, an AThook protein, is necessary for the negative feedback of
  134. (2004). Yang C: Plant gametogenesis: conservation and contrasts in development. Reproduction

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.