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Research ArticleDEVELOPMENT AND HORMONE ACTION
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Microarray Analysis of Brassinosteroid-Regulated Genes in Arabidopsis

Hideki Goda, Yukihisa Shimada, Tadao Asami, Shozo Fujioka, Shigeo Yoshida
Hideki Goda
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Yukihisa Shimada
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Tadao Asami
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Shozo Fujioka
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Shigeo Yoshida
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Published November 2002. DOI: https://doi.org/10.1104/pp.011254

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  • Fig. 1.
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    Fig. 1.

    Comparison of BL treatment on the WT,bri1, and det2 seedlings with the use of GeneChip. A, The distribution of the signal log ratio values for WT (y axis) and det2 (x axis) are shown for the BR-regulated genes, listed in Tables I to III. B, The distribution of signal log ratio values for bri1(y axis) and det2 (x axis) are shown for the BR-regulated genes, listed in Tables I to III. The signal log ratio represents the ratio of hybridization signals between BL- and mock-treated samples using a log (base 2) scale. A signal log ratio of 1 represents a gene that shows a 2-fold increase in expression by BL treatment; a signal log ratio of −1 represents a gene that shows a 2-fold reduction by BL treatment.

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    Fig. 2.

    Comparison of BL and Brz treatment with the use of GeneChip experiment. The distribution of signal log ratio values for treatments with BL (y axis) and Brz (x axis) are shown. A, All of the genes (>8,000) on the GeneChip are plotted. B, Genes that are induced or reduced more than 2-fold in a single GeneChip experiment are plotted. C, Genes that are induced or reduced more than 2-fold in two of the three GeneChip experiments are plotted. D, The BR-regulated genes (induced or reduced more than 2-fold in three GeneChip experiments, listed in Tables I and II) are plotted. The signal log ratio represents the ratios of hybridization signals using a log (base 2) scale. A signal log ratio of 1 represents a gene whose expression is increased 2-fold by treatment with either BL or Brz, and a signal log ratio of −1 represents a gene whose expression is reduced 2-fold by treatment with either BL or Brz.

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    Fig. 3.

    Regulation of PIF3, Lhcb1.3, and rbcS-1A gene expression by BL. Time courses of the inhibition of PIF3 (A), Lhcb1.3 (B), andrbcS-1A (C) gene expression by BL. Light-growndet2 seedlings were treated with 10 nmBL or were mock treated (cont) for the indicated times, and transcript abundance was analyzed by quantitative Taq-Man RT-PCR. D, Effects of cycloheximide (CHX) on PIF3 expression. Seedlings were treated with 100 μm CHX or mock treatment for 1 h, and then for an additional 3 h with 10 nm BL or mock treatment in the continued presence of CHX. The amount of PIF3 mRNA was determined by quantitative Taq-Man RT-PCR analysis. Transcript abundance levels are presented as relative values that are normalized with respect to the levels of 18S ribosomal RNA. Data are means ±se from three different plant samples.

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    Fig. 4.

    Induction of early auxin-inducible genes by BL. Kinetics of the induction of a GH3 homolog, BRU6(A), SAUR-AC1 (B), and IAA3 (C) by BL are shown. Light-grown det2 seedlings were treated with 10 nm BL or were mock treated (cont) for the indicated times, after which transcript abundance was analyzed by Taq-Man RT-PCR. Transcript abundance levels are presented as relative values that are normalized with respect to the levels of 18S ribosomal RNA. Data are means ± se from three different plant samples.

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    Fig. 5.

    BL induction of genes that are implicated in cell elongation or cell wall organization. Kinetics of induction by BL ofTCH4 (A), a putative expansin gene AtExp8 (B), and KCS1 (C) are shown. Light-grown det2seedlings were treated with 10 nm BL or were mock treated (cont) for the indicated times, after which transcript abundance was analyzed by Taq-Man RT-PCR. Transcript abundance levels are presented as relative values that are normalized with respect to the levels of 18S ribosomal RNA. Data are shown as means ± se from three different plant samples.

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    Fig. 6.

    Regulation of P450 genes by BL. A, Phylogenetic relationships among BR-regulated and other P450 genes. Proteins whose genes were shown to be up- or down-regulated by BL are indicated in bold and underlined, respectively (Tables I andII). BR6ox (Arabidopsis, CYP85A, AB035868), CPD (Arabidopsis, CYP90A,X87367), ROT3 (Arabidopsis, CYP90C, AB008097), DWF4 (Arabidopsis, CYP90B, AF044216), and CYP90D (Arabidopsis, AB066286) belong to the CYP85 or CYP90 families. CYP72B1 (Arabidopsis, BAS1, AC003105) is a suppressor of the phyB mutant. CYP88A3 (Arabidopsis, AtKAO1,AF318500) and CYP701A3 (Arabidopsis, GA3, AF047720) participate in GA biosynthesis. CYP83B1 (Arabidopsis, D78598) and CYP79B2 (Arabidopsis, AF069495) participate in auxin metabolism. The genes for CYP73A1 (Helianthus sp., cinnamate 4-hydroxylase,Z17369) and CYP75A1 (Petunia sp., flavonoid-3′, 5′-hydroxylase, D14588) were the first P450 genes to be identified functionally in higher plants and belong to the higher plant-specific group A of P450 genes. The accession numbers of the other P450 family members are D30718 (CYP8) and M93133 (CYP7A1). Kinetics of regulation of the CPD (B), DWF4 (C), BR6ox (D),ROT3 (E), CYP90D (F), CYP72, CYP85, CYP90, andBAS1 (G) genes by BL are shown. Light-grown det2seedlings were treated with 10 nm BL or were mock treated (cont) for the indicated times, after which transcript abundance was analyzed by Taq-Man RT-PCR. Transcript abundance levels are presented as relative values that are normalized with respect to the levels of 18S ribosomal RNA. Data are shown as means ±se from three different plant samples.

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    Fig. 7.

    Frequencies of up-regulated and down-regulated genes. A, Distribution of BR-down-regulated genes that are listed in Table I. B, Distribution of BR-up-regulated genes that are listed in Table II. The BR-regulated genes are classified into the functional categories based on their established or putative functions.

Tables

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    Table I.

    Genes down-regulated by BRs in the det2 mutant

    Gene NameAccession No.Function or CommentAffymetrix No.det2WT
    AmplifiedNo-Amp.AmplifiedNo-Amp.
    FC ± seFC ± seFC ±seFC ± se
    DWF4/CYP90B1 AF044216 BR biosynthesis (P450)13870_at−7.5 ± 0.76−3.4 ± 0.29−2.8 ± 0.40−1.8 ± 0.10
    CPD/CYP90A1 X87367 BR biosynthesis (P450)16042_s_at−2.5 ± 0.66−3.7 ± 0.37−4.0 ± 1.30−4.0 ± 0.40
    ROT3/CYP90C1 AB008097 Leaf polar elongation (P450)16535_s_at−4.5 ± 0.45−3.8 ± 0.17−2.1 ± 0.10−2.3 ± 0.05
    CYP71B3 D78602 Expression in older leaves (P450)17039_at−2.6 ± 0.20−2.3 ± 0.49−2.3 ± 0.80−1.3 ± 0.25
    PIF3 AF100166 PIF314630_s_at−2.1 ± 0.07−2.1 ± 0.09−1.1 ± 0.05−0.1 ± 1.05
    NIA1/NR1 X13434 Nitrate reductase (cytokinin-regulated type)14240_s_at−3.0 ± 0.62−4.0 ± 0.32−4.2 ± 0.15−4.6 ± 0.05
    XTR7 U43489 Putative xyloglucan endotransglycosylase15178_s_at−3.1 ± 0.46−3.5 ± 0.55−1.7 ± 0.05−1.5 ± 0.00
    AAP3 X77499 Amino acid transporter (His uptake complement)12372_at−4.5 ± 0.59−4.5 ± 0.99−2.0 ± 0.10−2.1 ± 0.05
    AAP4 X77500 Amino acid transporter (His uptake complement)16522_at−2.3 ± 0.12−2.4 ± 0.35−1.7 ± 0.10−2.0 ± 0.05
    AtKUP1 AF029876 High-affinity potassium transporter16119_s_at−6.5 ± 0.56−6.3 ± 0.50−2.3 ± 0.00−2.2 ± 0.30
    AKT2 U40154 Potassium channel16163_s_at−4.4 ± 0.71−2.6 ± 0.23−2.5 ± 0.10−1.7 ± 0.00
    AtNAS1 AB021934 Nicotianamine synthase20547_at−3.3 ± 0.12−3.3 ± 0.31−2.2 ± 0.20−2.3 ± 0.25
    AtmybL2 Z68157 Leaf-specific myb-related protein20362_at−2.9 ± 0.42−2.5 ± 0.33−2.1 ± 0.70−1.9 ± 0.55
    Athb-5 X67033 Athb family Leu-zipper protein20389_at−2.4 ± 0.12−2.2 ± 0.31−2.4 ± 0.25−2.1 ± 0.00
    MS2-like protein X99923 Fatty acyl CoA reductase homolog19177_at−2.9 ± 0.43−3.3 ± 0.35−8.7 ± 2.60−4.6 ± 2.10
    CYP78A6 AC006418/F13A10.19P450 monooxygenase18190_at−7.3 ± 0.73−2.9 ± 0.59−3.7 ± 0.50−1.5 ± 0.30
    CYP81H1 Z99707/C7A10.50P450 monooxygenase20271_at−3.5 ± 0.18−3.1 ± 0.59−2.6 ± 0.00−1.5 ± 0.35
    CYP710A AC004481/F13P17.32P450 monooxygenase14856_at−4.1 ± 0.20−4.4 ± 0.50−3.9 ± 0.05−3.4 ± 0.60
    CYP96A1 AC002391/T20D16.19P450 monooxygenase19281_i_at−3.2 ± 0.12−2.5 ± 0.65−2.0 ± 0.40−1.9 ± 0.55
    CYP96A9 AL078620/F23D16.110P450 monooxygenase19730_at−2.5 ± 0.23−2.2 ± 0.38−1.5 ± 0.00−1.6 ± 0.00
    PAP1/IAA26 AF088281 IAA gene family/putative phytochrome-associated protein16078_at−3.4 ± 0.49−2.7 ± 0.07−2.6 ± 0.20−2.7 ± 0.25
    iaglu U81293 Putative indole-3-acetate β-d-glucosyltransferase16603_s_at−3.1 ± 0.42−2.9 ± 0.24−1.3 ± 0.20−1.4 ± 0.15
    PIN7 AF087820 Putative auxin efflux carrier protein17576_at−2.2 ± 0.06−2.2 ± 0.17−1.7 ± 0.00−1.6 ± 0.00
    MYB55 AF176000 MYB-like gene17977_at−5.0 ± 0.37−4.5 ± 1.00−3.7 ± 0.95−2.4 ± 0.05
    BRD1 AL049746/T23J7.130Aldose 1-epimerase like protein12998_at−2.5 ± 0.20−2.3 ± 0.38−2.0 ± 0.00−1.7 ± 0.10
    BRD2 AC006836/F19B11.20Putative sulfotransferase19127_at−2.5 ± 0.29−2.5 ± 0.29−2.0 ± 0.10−2.2 ± 0.35
    BRD3 AL049171/T25K17.30Putative caffeoyl-CoA O-methyltransferase19348_at−2.3 ± 0.25−2.3 ± 0.26−1.2 ± 0.050.0 ± 1.15
    BRD4 AL035528/F18A5.290Leu-rich repeat protein14110_i_at−4.0 ± 0.35−1.9 ± 0.38−2.0 ± 0.10−1.3 ± 0.10
    BRD5/SAUR361-a AC002387/F4L23.28Auxin-inducible SAUR gene homolog14448_at−4.4 ± 0.85−2.9 ± 0.70−3.0 ± 0.20−1.7 ± 0.25
    BRD6 AL049659/T29H11.120Putative DNA-binding protein (BTB domain)19977_at−4.1 ± 0.47−3.8 ± 0.50−2.1 ± 0.30−2.3 ± 0.50
    BRD7 AC002335/T01O24.18MYB-like gene18780_at−4.2 ± 0.82−2.7 ± 0.15−2.2 ± 0.45−1.2 ± 0.05
    BRD8 AC007659/T14P1.14GATA-type zinc finger protein13168_i_at−2.2 ± 0.13−2.2 ± 0.06−1.6 ± 0.05−1.7 ± 0.35
    BRD9 Z99708/C7A10.580Unknown19221_at−3.2 ± 0.15−3.1 ± 0.23−2.4 ± 0.40−2.4 ± 0.15
    BRD10 AL035605/F19F18.30Unknown19398_at−2.9 ± 0.18−2.9 ± 0.15−2.2 ± 0.05−2.3 ± 0.10
    BRD11 AC006224/MFL8.8Unknown20174_at−5.2 ± 0.27−4.2 ± 0.46−3.6 ± 0.45−2.4 ± 0.15
    BRD12 AC003033/T21L14.19Unknown19889_at−2.6 ± 0.22−2.5 ± 0.28−0.1 ± 1.35−0.1 ± 1.15

    When genes have names on publications or on database, we adopted their names. Otherwise, we designated genes from BRD1 to BRD12. Amplified and No-Amp., Before and after signal amplification with antibody, respectively.

      • ↵F1-a  Gene name for SAUR36 is from Hagen and Guilfoyle (2002).

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      Table II.

      Genes up-regulated by BRs

      Gene NameAccession No.Function or CommentAffymetrix No.det2WT
      AmplifiedNo-Amp.AmplifiedNo-Amp.
      FC ± seFC ± seFC ±seFC ± se
      IAA3/SHY2 U18406 Auxin-inducible nuclear protein/suppressor of phyB13301_at2.4 ± 0.422.7 ± 0.291.3 ± 0.101.3 ± 0.10
      IAA5 U18407 Auxin-inducible nuclear protein13660_i_at16.8 ± 4.647.8 ± 1.023.3 ± 0.351.8 ± 0.00
      SAUR-AC1/−15 S70188 Small auxin up RNA from Arabidopsis Columbia12608_i_at9.9 ± 0.559.6 ± 1.223.3 ± 0.003.7 ± 0.25
      IAA19 U49075 Member of IAA gene family/IAA1 binding protein13296_at3.1 ± 0.252.9 ± 0.151.8 ± 0.002.1 ± 0.20
      BAS1/CYP72B1 AC003105/F18A8.8Activation-tagged suppressor of phyB12543_at3.8 ± 0.274.2 ± 1.162.7 ± 0.053.1 ± 0.00
      TCH2 AF026473 Touch-induced gene 2/calmodulin-related protein18300_at2.5 ± 0.192.7 ± 0.241.9 ± 0.151.8 ± 0.05
      TCH4 AF051338 Touch-induced gene 4/xyloglucan endotransglycosylase16620_s_at8.8 ± 0.8116.8 ± 4.626.5 ± 0.358.2 ± 0.75
      XTR6 U43488 Xyloglucan endotransglycosylase-related protein 617533_s_at9.0 ± 1.105.7 ± 0.965.5 ± 0.451.4 ± 2.50
      MSS3 AC004450/F14B2.23Suppressor of snf4/calmodulin-like protein (EF-hand)20689_at3.2 ± 0.353.8 ± 0.581.6 ± 0.151.8 ± 0.25
      ZAT7 X98676 Zinc finger protein15778_at4.2 ± 0.472.0 ± 0.151.4 ± 0.150.1 ± 1.20
      ATPA2 X99952 Root-specific peroxidase12356_at4.0 ± 2.093.0 ± 0.431.4 ± 0.201.7 ± 0.40
      KCS1 AF053345 Fatty acid elongase 3-ketoacyl-CoA synthase 117961_at2.7 ± 0.283.0 ± 0.291.3 ± 0.051.3 ± 0.10
      OPR1 U92460 12-Oxophytodienoate reductase (jasmonate biosynthesis)18253_s_at2.0 ± 0.032.1 ± 0.031.4 ± 0.101.4 ± 0.10
      AtPMEpcrB AF033206 Pectin methylesterase homolog19267_s_at4.1 ± 0.324.4 ± 0.463.3 ± 0.153.5 ± 0.10
      ATP24a Y11788 Peroxidase18946_at2.3 ± 0.152.4 ± 0.300.0 ± 1.051.1 ± 0.05
      CYP94C1 AC005824/F15K20.21P450 monooxygenase19288_at10.1 ± 3.324.0 ± 0.972.0 ± 0.201.7 ± 0.25
      CYP86A2 AF013293/A_IG005I10.21P450 monooxygenase17966_at2.0 ± 0.092.2 ± 0.151.3 ± 0.001.3 ± 0.00
      BRU2/SAUR-25 AL035528/F18A5.180Auxin-inducible SAUR gene family13395_at5.3 ± 0.632.6 ± 0.381.6 ± 0.051.6 ± 0.50
      BRU3/SAUR-9 AL022373/T19K4.240Auxin-inducible SAUR gene family12947_at9.0 ± 0.219.2 ± 0.654.9 ± 0.354.9 ± 0.20
      BRU4/SAUR16 AL035656/T9A14.140Auxin-inducible SAUR gene family13322_at5.8 ± 0.686.5 ± 1.002.2 ± 0.052.5 ± 0.30
      BRU5/SAUR-10 AC006201/T27K22.12Auxin-inducible SAUR gene family13781_at3.0 ± 0.663.0 ± 0.061.6 ± 0.151.7 ± 0.20
      BRU6/GH3-22-a AL035601/F6G17.40Auxin-inducible GH3 gene family13565_at2.3 ± 0.172.2 ± 0.151.3 ± 0.051.8 ± 0.35
      BRU7/GH3-10 AC005275/F4C21.36Auxin-inducible GH3 gene family13812_at2.2 ± 0.212.3 ± 0.151.7 ± 0.201.8 ± 0.40
      BRU8 AC004512/T8F5.9Putative xyloglucan endotransglycosylase (TCH4 homolog)17960_at7.7 ± 0.488.0 ± 0.432.1 ± 0.352.0 ± 0.30
      BRU9 AC007067/T10O24.17Putative endoxyloglucan transferase (EXGT-A3 homolog)19490_at22.0 ± 9.1710.9 ± 2.545.2 ± 0.103.7 ± 0.00
      AtExp8 AC002336/T2P4.4Putative expansin (expansin2-homolog)19660_at3.3 ± 0.573.7 ± 0.571.3 ± 0.051.3 ± 0.05
      BRU11 AL035539/F22I13.170Putative expansin (pollen allergen protein homolog)19976_at6.2 ± 0.427.2 ± 0.922.0 ± 0.002.1 ± 0.10
      BRU12 AC005169/F6F22.19Putative extensin with Leu-rich repeat (LRX1 homolog)18525_at3.3 ± 0.092.4 ± 0.451.3 ± 0.20−0.1 ± 1.10
      BRU13 AC005698/T3P18.1Putative extensin with Leu-rich repeat (LRX1 homolog)18998_at2.2 ± 0.152.3 ± 0.292.0 ± 0.402.0 ± 0.50
      BRU14 AL049608/T9E8.80Putative extensin with Leu-rich repeat (LRX1 homolog)20537_at2.8 ± 0.153.1 ± 0.151.6 ± 0.001.8 ± 0.00
      BRU15 AC003027/F21M11.20Putative arabinogalactan protein (fasciclin-domain)16438_at0.6 ± 0.802.2 ± 0.101.6 ± 0.101.7 ± 0.10
      BRU16 AL035601/F6GT17.100Putative arabinogalactan protein14947_at1.5 ± 0.282.5 ± 0.181.8 ± 0.001.8 ± 0.00
      BRU17 AF060874 Putative arabinogalactan protein (AtAGP4 homolog)15107_s_at1.7 ± 0.372.4 ± 0.241.5 ± 0.001.5 ± 0.00
      BRU18 AF069298/T14P8.14Putative pectinesterase14612_at4.0 ± 0.184.2 ± 0.263.3 ± 0.403.6 ± 0.55
      BRU19 AL022580/T5K18.200Putative pectinacetylesterase19905_at3.0 ± 0.283.6 ± 0.732.5 ± 0.453.3 ± 0.95
      BRU20 AC004077/T31E10.15Endo-1,4-β-xylanase homolog15271_at2.7 ± 0.172.9 ± 0.121.5 ± 0.051.6 ± 0.10
      BRU21 AL030978/M4122.170Ca2+-binding protein homolog15431_at3.1 ± 0.253.6 ± 0.492.3 ± 0.102.2 ± 0.00
      BRU22 AL022198/F6I18.90Putative calmodulin-binding protein19857_at2.7 ± 0.202.7 ± 0.171.7 ± 0.102.0 ± 0.20
      BRU23 AC005970/T6P5.14Putative protein kinase14030_at2.2 ± 0.102.4 ± 0.331.5 ± 0.151.7 ± 0.15
      BRU24 AC002339/T11A7.8Putative receptor kinase (CLV1 homolog)14112_at3.4 ± 0.902.4 ± 0.321.7 ± 0.251.8 ± 0.10
      BRU25 AC004238/F19I3.16Leu-rich repeat domain12251_at4.5 ± 0.674.7 ± 0.723.5 ± 0.852.6 ± 0.25
      BRU26 AC002354/F6P23.7NAM/NAC gene homolog13806_at2.9 ± 0.443.0 ± 0.701.8 ± 0.301.6 ± 0.05
      BRU27 AC006533/F20M17.23Ethylene-Regulated protein ER33 homolog15403_s_at3.7 ± 0.253.8 ± 0.291.9 ± 0.152.1 ± 0.20
      BRU28 AF128396/T3H13.3Phosphate-induced gene phl-1 homolog14077_at3.2 ± 0.355.8 ± 0.293.6 ± 0.303.5 ± 0.30
      BRU29 AL021711/F13C5.140Pro-rich protein (APG) homolog (GDSL-motif)16434_at2.8 ± 0.153.0 ± 0.032.4 ± 0.402.4 ± 0.35
      BRU30 AL035353/F16A16.110Pro-rich protein (APG) homolog (GDSL-motif)17196_at3.9 ± 0.384.7 ± 0.481.9 ± 0.202.3 ± 0.25
      BRU31 AC005917/F3P11.22Pollen-specific protein (SF21) homolog15892_at2.4 ± 0.182.7 ± 0.321.8 ± 0.151.8 ± 0.25
      BRU32 AC005679/F9K20.9Carrot (Daucus carota) EP1 homolog17440_i_at2.7 ± 0.323.2 ± 0.551.6 ± 0.201.6 ± 0.25
      BRU33 AC007060/T5I8.14Phosphatidylinositol/phosphatidylcholine transfer protein homolog12046_at3.6 ± 0.343.8 ± 0.251.9 ± 0.101.9 ± 0.15
      BRU34 AP007269/A_IG002N01.14Unknown12953_at3.1 ± 0.353.3 ± 0.491.6 ± 0.051.8 ± 0.05
      BRU35 AC005169/F6F22.17Unknown13916_at2.2 ± 0.123.6 ± 0.203.6 ± 0.203.8 ± 0.45
      BRU36 AC005106/T25N20.6Unknown14913_at3.7 ± 0.343.4 ± 0.470.1 ± 1.050.0 ± 1.10
      BRU37 AL049481/T5L19.20Unknown14951_at2.6 ± 0.262.8 ± 0.322.0 ± 0.102.2 ± 0.20
      BRU38 AC002535/T30B22.26Unknown19880_at2.6 ± 0.152.9 ± 0.251.6 ± 0.201.6 ± 0.10
      BRU39 AC007138/T7B11.21Unknown19992_at3.0 ± 0.213.4 ± 0.321.6 ± 0.101.6 ± 0.05
      BRU40 AL022224/F1C12.90Unknown12027_at2.8 ± 0.322.5 ± 0.541.2 ± 0.050.0 ± 1.05
      BRU41 AC000348/T7N9.22Unknown14443_at2.1 ± 0.172.1 ± 0.121.8 ± 0.202.0 ± 0.25
      BRU42 AC006921/F2H17.17Unknown18885_at2.0 ± 0.122.1 ± 0.122.0 ± 0.002.2 ± 0.10
      BRU43 AC004521/F411.31Unknown12584_at2.1 ± 0.152.8 ± 0.571.4 ± 0.101.5 ± 0.45

      When genes have names on publications or on database, we adopted their names. Otherwise, we designated genes from BRU2 to BRU43. Ampified and No-Amp., Before and after signal amplification with antibody, respectively.

        • ↵F2-a  Gene names for SAUR and GH3 genes are from Hagen and Guilfoyle (2002).

        • View popup
        Table III.

        Genes down-regulated by BRs in WT

        Gene NameAccession No.Function or CommentAffymetrix No.det2WT
        AmplifiedNo-Amp.AmplifiedNo-Amp.
        FC ± seFC ± seFC ±seFC ± se
        CYP79B2 AF069495 Cytochrome P45020479_i_at−0.4 ± 0.70−0.4 ± 0.68−1.6 ± 0.35−2.2 ± 0.05
        CYP81D8 AL035601/F6G17.20Cytochrome P45014032_at−2.0 ± 0.50−0.7 ± 1.07−3.7 ± 0.20−1.9 ± 0.15
        4HPPD AF047834 4-Hydroxyphenylpyruvate dioxygenase15669_s_at−2.4 ± 0.30−2.3 ± 0.30−6.9 ± 1.60−3.0 ± 0.30
        CHI M86358 Chalcone isomerase20413_at−1.4 ± 0.15−1.3 ± 0.12−2.2 ± 0.05−2.3 ± 0.45
        BRI1 AF017056 BRI120209_at−1.8 ± 0.06−1.9 ± 0.13−2.0 ± 0.05−2.0 ± 0.20
        Eli3-1 X67816 Cinnamyl-alcohol dehydrogenase13242_at−1.9 ± 0.25−1.9 ± 0.15−1.7 ± 0.00−2.1 ± 0.05
        BRD13 AL021713/T9A21.60Putative protein13514_s_at−1.9 ± 0.74−1.8 ± 0.03−4.0 ± 0.50−2.0 ± 0.35
        BRD14 AC006085/F11M15.3Putative Ser/Thr protein kinase16878_at−3.3 ± 0.56−1.8 ± 0.74−4.0 ± 0.10−1.8 ± 0.00
        BRD15 AC012562/F17O14.23Osmotic stress-inducible kinase like-protein13246_at−1.8 ± 0.39−0.6 ± 0.83−3.8 ± 1.10−1.9 ± 0.70
        BRD16 AL049480/F14M19.60Putative pathogenesis-related protein18755_at−2.1 ± 0.38−2.0 ± 0.68−2.6 ± 0.50−2.0 ± 0.25
        BRD17 AL033545/F7K2.50Extensin-like protein12115_at−2.2 ± 0.19−1.8 ± 0.10−2.4 ± 0.25−2.3 ± 0.05
        BRD18 AC005662/F13H10.7Putative embryo-abundant protein14083_at−2.0 ± 0.15−1.8 ± 0.27−2.4 ± 0.15−2.2 ± 0.15
        BRD19 Y12776 Late embryogenesis-abundant protein like-protein18594_at−1.5 ± 0.09−1.6 ± 0.09−2.1 ± 0.05−2.0 ± 0.00
        BRD20 AL021811/F10M6.70Putative protein14574_at−2.8 ± 0.38−2.4 ± 0.52−1.8 ± 0.15−2.2 ± 0.15
        BRD21 AC007661/T8P21.9Putative protein15487_at−1.6 ± 0.12−1.6 ± 0.29−1.8 ± 0.55−2.1 ± 0.05

        When genes have names on publications or on database, we adopted their names. Otherwise, we designed genes from BRD13 to BRD21. Amplified and No-Amp., before and after signal amplification with antibody, respectively.

          • View popup
          Table IV.

          Chlorophyll contents after BL treatment

          Chl aChl bChl a/b
          mg g−1 fresh wt.
          BL0.26 ± 0.040.08 ± 0.013.22 ± 0.04
          Cont0.50 ± 0.030.16 ± 0.013.19 ± 0.06

          Data are means ± se. Chl, Chlorophyll.

            • View popup
            Table V.

            Primers and TaqMan probes used for RT-PCR

            Gene NameForward Primer SequenceReverse Primer SequenceTaqMan Probe Sequence
            CPDCCCAAACCACTTCAAAGATGCTGGGCCTGTCGTTACCGAGTTTCTGCCATCTCCAAGGGTTGAAAGTGC
            DWF4GTGATCTCAGCCGTACATTTGGACACGTCGAAAAACTACCACTTCCTCAGCAAAACAACGGAGCGTCATCG
            ROT3ATTGGCGCGTTCCTCAGATCAAGACGCCAAAGTGAGAACAACTCACCTCAAAGACCGGATCACTCGAGA
            BR6oxTGGCCAATCTTTGGCGAATCCCGTATCGGAGTCTTTGGTACCGAGTTTCTCAAACAAGGCCCCAAC
            CYP90DCTCATTACCCTTGCCGTCAAACAGCTTCATGTTTTCTTCCGTTAGCCTCTCTGATTCTCCTGCTGCCCTCAAT
            BAS1TTGGCTTCATACCGTTTGGCTTACAGCGAGTGTCAATTTGGCCGGAGTTCGTACATGCATTGGTCAGAATC
            Lhcb1.3GGAGCTCAAGAACGGAAGATTGGGTTCTCTATCGGTCCCTTACCATGGATTCTTCGTTCAAGCCATCGTCA
            rbcS1AGCTCTCTTCCGCTACTATGGTTGAAGGCAGCGGAGGACTTAAGTTCAGGCCACTATGGTCGCTCCTTTCA
            TCH4CAAGAACATGGAGTCTCTAGGCACTGTGAAAGGAGCTTTAGACCAATCGACTCGAGTCTTTGGAACGCTGATGATTGG
            PIF3TCAGGCTCACCAAAGCTAAGCCACACCAGCTCCACAACTTCAAATCTGCTCAAGACAGGAACCCTTCTCCAC
            GH3 homolog (BRU6)CGTATATCCAACGGCGATTGTCCAGCAGATGTTCCTGAGCTTTCTTCTCACCCCATCACCGAGTTTCTCA
            SAUR-AC1GAGGATTCATGGCGGTCTATGGTTAAGCCGCCCATTGGATTGGTGCCGGTTTCATACTTAAACCAGCCT
            IAA3AGCCTAAACCTTTGGCTTCTGAGGTGATTGGATGCTCATTGGTCTTGCACGTACATATGAACATCTCCCATGG
            XTR7TCGACGAGTTTGACCTCACTTGGTCCAGCGACAAAGACAGCATAACCACAGAGGCAAAATCTTCAACGGAGG
            AtExp8CAACCATCACCGTCACAGCTATGAAGAGGAGGATTGCACCAAAAACTTTTGCCCACCTAACCCTGGCCT
            KCS1GCTCAAATACGTGAAGCTTGGACAGCACGGTTCCGGTTAAACAACTCTTGCAACGTGACCACCATTCTCT
            18S ribosomal RNACGGCTACCACATCCAAGGAAGCTGGAATTACCGCGGCTTGCTGGCACCAGACTTGCCCTC
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          Microarray Analysis of Brassinosteroid-Regulated Genes in Arabidopsis
          Hideki Goda, Yukihisa Shimada, Tadao Asami, Shozo Fujioka, Shigeo Yoshida
          Plant Physiology Nov 2002, 130 (3) 1319-1334; DOI: 10.1104/pp.011254

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          Microarray Analysis of Brassinosteroid-Regulated Genes in Arabidopsis
          Hideki Goda, Yukihisa Shimada, Tadao Asami, Shozo Fujioka, Shigeo Yoshida
          Plant Physiology Nov 2002, 130 (3) 1319-1334; DOI: 10.1104/pp.011254
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