Supplemental Figure 1. Rosette Leaf Morphology of Single, Double and Triple Mutants of eid3, phya-201 and phyb-5. Photographs of Ler wild type,

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1 Supplemental Figure 1. Rosette Leaf Morphology of Single, Double and Triple Mutants of eid3, phya-201 and phyb-5. Photographs of Ler wild type, phya-201, phyb-5, phya-201 phyb-5, eid3, phya-201 eid3, phyb-5 eid3 and phya-201 phyb-5 eid3 plants grown under short day conditions (8 h white light / 16 h darkness) for eight weeks. Bar = 5 cm..

2 Supplemental Figure 2. Degradation and Sub-cellular Localization of PhyA in the eid3 Mutant Background. A, Immunoblot analyses of phya protein degradation. To follow phya degradation, 4-day-old etiolated Ler wild type and eid3 mutant seedlings were transferred to strong continuous red light (cr). Samples were taken before exposure to light (0 h) or at the given time points. Extraction of crude proteins and protein assays were performed as described by Dieterle et al. (2005) using 20 µg of total protein extracts. Immunodetection of phya was done using a specific antiserum. B, Epifluorescence microscopy analyses of the sub-cellular localization of phya-yfp in hypocotyl cells in wild type and eid3. For epifluorescence and light microscopy, seedlings were transferred to glass slides under dim-green safe light and analyzed with an Axioskop microscope (Zeiss, Oberkochem, Germany). The nuclei were located under dim-green safe light and only the first pictures taken with a digital Axiocam camera system (Zeiss) are presented. Excitation and detection of the fluorophore YFP was performed with a YFP-specific filter set (AHF Analysentechnik, Tübingen, Germany). Formation early nuclear speckles (enus) and sequestered areas of phya (SAP) were induced by irradiation with microscopic light. cd, continuous darkness; cfr, continuous far-red light; lnus, late nuclear speckles; nu, nucleus. Bar = 20 µm.

3 Supplemental Figure 3. Rosette Leaf Morphology of Single, Double and Triple Mutants of eid3, eid1-1, phya-401, and cop1 eid6. Photographs of Ler wild type, eid1-1, phya-401, cop1 eid6, eid3, eid3 eid1-1, eid3 phya-401, and cop1 eid6 eid3 plants grown under short day conditions (8 h white light / 16 h darkness) for eight weeks. Bar = 5 cm.

4 Supplemental Figure 4. Mapping of the eid3 Mutation. F2 seedlings from a cross of phyb-5 eid3 (Ler) with phyb-9 (Col) were used for fine mapping experiments. Because of the dominant eid3 phenotype, mapping was done using seedlings with wild type phenotype, indicative for the presence of two copies of the recessive Col wild type allele. Molecular markers show co-segregation of the eid3 locus with the m235 and nga248 markers (Supplemental Table S9) on chromosome 1 downstream of the PHYA Gene (AT1G09540). Recombination rates between mutant and Col wild type alleles are given in brackets.

5 Supplemental Figure 5. Expression of the Light-induced HY5 Marker Gene in Completely Etiolated eid3 Seedlings. A, Light-independent transcript accumulation of HY5 in the eid3 mutant cannot be suppressed by irradiation with extreme far-red light (RG9). Ler wild type and eid3 mutant seedlings were grown in darkness for 4 days after induction of germination using 10 µm gibberellic acid (+GA) without light treatment. Seeds were irradiated with a saturating RG9 pulse 2 or 3 hours after the GA treatment to photoconvert all Pfr, which could have remained from seed development, back to Pr. The gel shows the representative result of n = 2 independent experiments. B, Lightindependent transcript accumulation of HY5 in the eid3 mutant does not depend on the presence of phya or phyb photoreceptors. Ler wild type, phya-201 phyb-5 (AB), eid3 and phya-201 phyb-5 eid3 (ABeid3) mutant seedlings were grown in darkness for 4 days after induction of germination using either 2 h red light (-GA) or 10 µm gibberellic acid (+GA) without light treatment. The gel shows the representative result of n = 2 independent experiments. HY5 transcript levels were monitored at the indicated time points using RT-PCR. ACTIN2 (ACT) transcript levels are shown as a constitutive control. Gels were stained with SYBR safe DNA gel stain. Images are shown inverted.

6 A 45 min cf 60 min cr 2 min Rp & 45 min cd % 20 4 %/13 % % %/14 % % %/13 % 473 this study 4 h cf 2 d cr 6 d cw/b/r/f % %/8 % % % %/15 % % % %/7 % % Jiao et al. (2005) B 45 min cf 60 min cr 2 min Rp & 45 min cd % 4 1 %/5 % % % 11 2 %/8 % % % 27 4 %/13 % 187 this study 4 h cf 2 d cr 6 d cw/b/r/f %/9 % %/9 % % %/5 % % Jiao et al. (2005) Supplemental Figure 6. Comparison of differentially regulated transcripts in etiolated eid3 with published data sets of light-regulated genes. Venn diagrams depict comparisons of differentially regulated transcripts in etiolated eid3 (black circles) with published microarray data (Jiao et al., 2005; Leivar et al., 2009; Peschke et al., 2011) from Arabidopsis seedlings subjected to various irradiation times under different light qualities (red circles). eid3 transcript accumulation patterns were also compared to data from 4-day-old, etiolated Ler wild type seedlings, which were treated with a saturating, 2-min long red-light-pulse before transfer back to darkness for 43 min (this study; Supplemental Tabs. S4, 5). Percentages were calculated according to total number of genes that exhibited significant up- or downregulation between etiolated eid3 seedlings and data sets of light-regulated genes. A, Up-regulated genes. B, Down-regulated genes. cd, continuous darkness; cf, continuous far-red light; cr, continuous red light; cw/b/r/f, continuous white/blue/red/far-red light; Rp, red-light pulse.