Supplemental Figure Legends
Figure S1 . ChIP-Seq confirms the binding of PRR7 to the promoters of CCA1 and LHY . Mapped
ChIP-Seq reads in Experiment II in the (a) CCA1 and (b) LHY promoter regions and their respective gene structures in prr7-3 PRR7::HA-PRR7 and prr7-3 immunoprecipitated samples.
Numbers in brackets on the left-hand side indicate the scale shown. Analysis of the association of PRR7 to specific regions in the (c) CCA1 and (d) LHY promoters by ChIP-qPCR using
35S::HA-PRR7 lines. Data are the average of 3-7 biological replicates

standard error.
(e) and (f) show the analysis of PRR7 binding to other putative targets identified by ChIP-Seq using ChIP-qPCR with the 35S::HA-PRR7 #54 line. Data represents the average

standard error of three biological replicates. The enrichments in HA-PRR7 samples were significantly different from the wild type in (e) (Student's t -test, p<0.05) but not in (f). The ACT2 intron was used as a control. Also indicated are the ChIP-Seq experiments from which the binding sites were initially identified.
Figure S2 . Expression of putative genes associated with PRR7 binding sites in wild type (Col-
WT), PRR7 overexpressor ( PRR7ox , 35S::HA-PRR7 #54) and the prr579 triple mutant. (a-h)
Analysis of pairs of genes associated with one binding site for which the binding site is located upstream (US, -1/-1000 from transcriptional start) of one of the genes and one downstream (DS,
+1/+1000 from transcriptional stop) of the other one. (i-k) Analysis of pairs of genes associated with one binding site for which the binding site is located upstream (US, -1/-1000 from transcriptional start) of both genes. The number in the top right corner of each panel represents the PRR7 binding site location (the average of both ChIP-Seq experiments or in case of (k), the location in Experiment II). (l-q) Expression of genes with a PRR7 binding site in their US region
(l, m, o, p, q) or 5'UTR region (n). Binding site rank number in Experiment II for the sites analyzed as reported in Dataset S1: (a) R-2; (b) R-25; (b) R-31; (d) R-42; (e) R-44; (f) R-315; (g)
R-110; (h) R-383; (i) R-47; (j) R-5; (k) R-319.The data are the average of 2-3 biological replicates

standard error. Expression level was analyzed by RT-qPCR and normalized to IPP2 .
(*) Indicate significant differences with the wild type ( t -test, p<0.05). The diagrams indicate the relative position of the binding sites (PRR7-BS) with respect to transcriptional start sites of associated genes.
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Figure S3.
Motifs significantly enriched at the common and independently confirmed PRR7 binding sites located upstream of a gene. (a) Regions of 200 bp (100 bp on either side) and (b)
500 bp (250 bp on either side) surrounding the PRR7 binding sites were used as input into
MEME. Numbers on top of the logos are the E-values for each of the different motifs.
Figure S4. TOC1 RNA levels in the presence or absence of exogenous ABA. Seedlings were treated with 10 µM ABA at ZT0. Data are the average 
standard error of 3 biological replicates.
Expression level was analyzed by RT-qPCR and normalized to IPP2 .
Figure S5 . CCA1 (a) and LHY (b) expression level in prr7,9 amiR CCA1 LHY lines. Seedlings were harvested at ZT0 and expression level was analyzed by RT-qPCR and normalized to IPP2 .
Data are the average

standard error of 3 biological replicates.
Figure S6 . Translatome data for (a) TOC1, (b) PRR5, (c) PRR7 and (d) PRR9. Data are derived from microarray studies of RNA bound to polysomes (http://efp.ucr.edu) (Mustroph et al., 2009).
Analysis is based on co-immunoprecipitation with tagged ribosomes expressed under the control of different cell specific promoters: pGL.2 for trichomes, pCER5 for epidermis, pRBCS for mesophyll, pSULTR2.2 for bundle sheath, pSUC2 for companion cells and pKAT1 for guard cells. The colors refer to expression levels, with yellow indicating low levels of expression and red corresponding to high levels of expression. Data are from plants grown under 16h light/8h dark photoperiods, and harvested at ZT18 after 2h of low light (Mustroph et al., 2009).
Figure S7. Schematic representation of sample comparisons for binding site identification using
QuEST and analysis of target genes identified in Experiment I and/or Experiment II. (a)
Schematic representation of samples compared for binding site identification in Experiment I and
Experiment II using QuEST. Numbers indicate number of binding sites. Bold labels indicate samples that were used as controls for QuEST analysis. Lines and numbers in gray are comparisons that were not used for further studies. (b) Percentage of genes that display increased expression levels in the prr579 mutant at ZT12 based on microarray analysis from reference
(Nakamichi et al., 2009). (c) Percentage of genes that display cycling expression levels. Data is
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from (Edwards et al., 2006) for LL (constant light) and (Blasing et al., 2005) for LD (light/dark).
Cycling gene expression was analyzed using PHASER (Michael et al., 2008). Genes were defined as cycling if the mbpma > 0.8. (d) PRR7 binding site location in Experiment I. (e) PRR7 binding site location in Experiment II. FDR, false discovery rate; E, exon; I, intron; Genome, all genes; Exp. I, genes associated with binding sites identified in Experiment I; Exp. II, genes associated with binding sites identified in Experiment II; Common, genes identified in both experiments in addition to genes identified in only one experiment but confirmed by ChIP-qPCR.
Fisher's-exact test: **, p<0.001; ***, p<0.0001.
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