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Figure S1. PIF5 binds with different frequency to various E-box sequences in vivo. PIF5 binding sites that were assigned to a gene locus were chosen. For each binding site the most central E-box was detected. Sequences with two E-boxes with the same distance to the peak summit were discarded from the analysis. E-box sequences were then counted and sense and antisense sequences as well as their reverse complements were grouped.

Figure S2. Chromatin Immunoprecipitation (ChIP) of PIF5-HA after 2 hours in low R/FR. Immunoprecipitated DNA was quantified by Q-PCR using primers in the promoter region containing a G-box or control region (minimum 1 kb 3’ or 5’ from the peak region). Data are average of technical triplicates of the Q-PCR. (A / B) Col and/or PIF5-HA lines were grown for 7 days in constant light conditions before being shifted for 2 hours in low R/FR conditions. (C) PIF5-HA lines were grown for 14 days in constant light conditions before being shifted for 2 hours in low R/FR conditions.

Table S1. List of genes with a PIF5 peak identified by ChIP sequ in the PIF5-HA line transfered for 2 hours into low R/FR.

Table S2. Lists of GO anaylsis. Sheet a : GO analysis of genes set identified by PIF5-HA ChIP-seq; sheet b : GO analysis of genes showing a significant interaction between WT and pif4pif5 when comparing gene expression in high versus low R/FR; sheet c: GO analysis of list and sublists for genes differentially expressed in high R/FR between WT and pif4pif5; sheet d: GO analysis of genes with close binding site for PIF5 and PIF1.

Table S3. List of genes showing an altered regulation of gene expression in pif4pif5 when comparing  seedlings grown in high versus low R/FR (interaction between the genetic backgrounds and environmental conditions).

Table S4. List of genes with altered expression in pif4pif5 compared to wild-type seedlings grown in high R/FR.

Table S5. Comparison between the genes we identified as requiring PIF4 and PIF5 for normal expression in high R/FR (Figure 5) and the genes whose expression correlates with growth and requires PIF4 and PIF5 identified by (Nozue et al. 2011).

Table S6. List of primers used in this study.

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