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1 DOI:.38/ncb54 sensitivity (+/-) 3 det- WS bri-5 BL (nm) bzr-dbri- bzr-d/ bri- g h i a b c d e f Hypcocotyl length(cm) 5 5 PAC Hypocotyl length (cm) PPZ PPZ En bes-d En bes-d En bes-d j k l bzr-d ga-3 Ler sly- ga-3 Ler+PAC bzr-d/ ga-3 BL (nm) Hypocotyl length (cm) bzr-d PAC (nm) det PAC det M det bri-5 PAC bri-5 M bri-5 BL (nm) Relative hypocotyl length Relatvie hypocotyl length 8 4 bzr-d bri- bzr-d/ bri- bzr-d PAC (nm) det det det PAC bri-5 bri-5 bri-5 PAC BL (nm) Figure S Active BZR/BES are required for promotion of cell elongation. (a) BR signaling is required for promotion of cell elongation. The seedlings of wild type ( and WS), det-, and bri-5 were grown on ½ MS medium with or without μm 3 and different concentrations of BL for 7 days under constant light. sensitivity was calculated as the average ratio of hypocotyl length of treated plants to untreated plants (ratio of indicate no response to ). (b, c) Active BZR is required for promotion of cell elongation. The seedlings of wild type (), bri-, bzr-d and bzr-d/bri- were grown in the dark for days on ½ MS medium containing μm PAC with or without μm 3. Error bars mean s.d. (n= plants) : Significant difference between with or without treatment. (p <.) (d) bzr-d partly suppressed ga-3 phenotype. Error bars mean s.d. (n=5 plants). : Significant difference between ga-3 and bzr-d/ga-3. (p <.). (e-g) Both bzr-d and bes-d are less sensitive to PAC. The seedlings of wild type ( and En), bzr-d, and bes-d were grown in the dark on ½ MS medium with or without different concentrations of PAC for days. Error bars mean s.d. (n=3 plants) : Significant difference between with or without PAC treatment. (p <.). (h, i) bes-d suppresses the -insensitivity phenotype of BR-deficient plants. The seedlings of En and bes-d were grown in the dark on ½ MS medium containing μm PAC, μm PPZ and with or without μm 3 for days. Error bars mean s.d. (n=5 plants) : Significant difference between with PAC or treatment with the respective mock treatment. (p <,) (j) BR promotes cell elongation in mutants. Wild type (Ler), ga-3, sly- were grown under light for 7 days with or without different concentrations of BL and μm PAC. Error bars mean s.d. (n= plants). (k, l) increases, but PAC decreases the BR sensitivity of det-. The seedlings of det- and bri-5 were grown on ½ MS medium (M), or medium containing μm PAC or μm 3 and different concentrations of BL under constant light for 7 days. Average hypocotyl lengths (k) and relative hypocotyl lengths to BLuntreated seedlings (l) were measured from at least 3 seedlings. Error bars mean s.d. (n=45 plants). Macmillan Publishers Limited. All rights reserved.

2 a det- bri b BL c BL pbzr BZR Non-specific band pbzr BZR d BL Ler rga4/gai-t spy-3 pbzr BZR Non-specific band Figure S BR and regulate BZR and independently. (a) Eightday old seedlings of wild type (), det- and bri- were treated with mock solution (-) or μm 3 (+) for hr. The immuno-blot was analyzed by anti- antibody. (b) Eight-day old seedlings were treated with μm 3, nm BL, or both, for hr, and analyzed by anti- and anti-bzr immunoblot. Ponceau S staining of the blots showed equal loading of all samples. (c) The pbzr:bzr-cfp transgenic plants were grown on medium containing μm PAC for 7 days, treated with μm 3 or mock solution for 3 hr, then with nm BL or mock solution for hr. The blot was analyzed by anti-gfp antibody. (d) Wild type (Ler and ), rga-4/gai-t, and spy-3 plants were grown on ½ MS medium for 7 days, then treated with nm BL or mock solution for hr. The immuno-blots were probed with anti-bzr antibody, and the phosphorylated BZR (pbzr) and unphosphorylated BZR (BZR) were detected as two distinct bands. A non-specific band is shown as loading control. Macmillan Publishers Limited. All rights reserved.

3 a BD-BZR BD-BES BD-ΔN b I BZR-ccFP -nyfp -nyfp RGL RGL BZR-ccFP I-nYFP I-nYFP RGL3 ADT7 BZR-ccFP IBH-nYFP IBH-nYFP c - Input pcnx5 Pull down piaa9 Pull down d - piaa9 Pull down Input - Figure S3 interacts with BZR and inhibits BZR DNA binding. (a) Yeast two hybrid assays of the interaction between BZR, BES and DELLAs in yeast. (b) Bimolecular fluorescence complementation (BiFC) assays of the in vivo protein interaction. Leaf epidermal cells of N. benthamiana were cotransformated with the indicated pairs of constructs. (c, d) - inhibits BZR DNA binding in vitro. (c) pre-incubated with or - was incubated with biotinylated DNA fragments from the CNX5 and IAA9 promoters immobilized on streptavidin beads. (d) pre-incubated with biotinylated DNA fragments from IAA9 promoters immobilized on streptavidin beads was incubated with or -. The DNA-bound proteins were immunoblotted using anti- antibody. 3 Macmillan Publishers Limited. All rights reserved.

4 PIF4! BZR! PIFs-! BZR-! PIF4 BZR 3 PIFs BZR Total gene numbers gene numbers Figure S4 Venn diagrams show genes among the gene sets that BZR and PIF4 bind to and/or regulate. The PIF4 and BZR s were identified by PIF4 ChIP-Seq and BZR ChIP-chip, respectively; PIFand BZR- genes were differentially expressed in pifq versus WT and in bzr-d/bri- versus bri- grown in the dark. - genes were differentially expressed in ga-3 versus WT in the dark. Numbers show the percentages of each gene set that are - genes. 4 Macmillan Publishers Limited. All rights reserved.

5 7 4 Fig. d IB: 7 Fig. e IB: 7 IB: MYC Fig. g 7 3 Fig. f 7 5 IB: 7 Fig. h Fig. s3c 7 IB: IB: IB: 75 Fig. sa 75 Fig. sb 5 37 Fig. sb 7 Fig. sc 5 5 IB: IB: IB: BZR 7 4 Fig. sd IB: BZR 7 Fig. s3d 7 4 Fig. s3d Figure S5 Full scan data of immunoblots. Red asterisks indicate the bands shown in the figures. 5 Macmillan Publishers Limited. All rights reserved.