ABA related genes are misregulated in <i>NF-Y</i> mutant lines.

<p>Gene expression in 24 hr post light incubation seeds analyzed by quantitative RT-PCR for A) <i>ABI3</i>, B) <i>ABI5</i>, C) <i>AIA</i>, D) <i>AIL</i>, E) <i>RAB18</i>, and F) <i>RD29B</i>. For each gene, the expression level in Col-0 was defined as 1. Data represent means and standard deviation of three replicates.</p

Misregulated genes in the <i>nf-yc triple</i> mutant have ABRE-like promoter elements.

<p>A) ABRE-like motif discovered through MEME analysis. B) Positional distribution of MEME motif within the promoter set. TSS - transcriptional start site. To help assess the relationships between Arabidopsis NF-Y proteins discussed here and below, note that phylogenetic trees were previously published <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059481#pone.0059481-Siefers1" target="_blank">[9]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059481#pone.0059481-Gusmaroli1" target="_blank">[76]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059481#pone.0059481-Gusmaroli2" target="_blank">[77]</a>.</p

Full length NF-YB2 is required for the ABF3 interaction.

<p>Y2H assays were performed between AD:ABF3 and DBD fused to: A) Full length NF-YB2 (AA 1–190), B2HFM (AA 26–121), B2N (AA 1–25), B2C (AA 122–190), B2N+B2HFM (AA 1–122), and B2HFM+B2C (AA 122–190); B) Chimeric constructs - full length NF-YB10 (AA1–228), NF-YB2/NF-YB10, NF-YB10/NF-YB2, NF-YB10N (AA1–27) and NF-YB10C (AA 123–228).</p

<i>NF-YB</i> overexpression results in late germination.

<p>A–B) <i>nf-yb2</i>, <i>nf-yb3</i> and <i>nf-yb2/b3</i> double mutants on B5 and B5+1 µM ABA media. C–D) <i>p35S::NF-YB2</i> and <i>p35S::NF-YB3</i> on B5 and B5+1 uM ABA media. Germination data is compilation of two experiments (total of n = 6 replicates per genotype) using independent sets of matched seeds. Each replicate contained at least 30 seeds. A Fisher’s Exact Test was performed for both mutants (no difference) and overexpression lines at 84 hrs post-incubation. Both overexpression lines were significantly different (p<0.01) from parental Col-0. Separate, independent <i>NF-YB</i> overexpression lines had similar results.</p

<i>NF-YC</i> are strongly expressed in embryos and the endosperm 24 hours post incubation in light.

<p>A,G) Col-0, B,H) NF-YB2, C,I) NF-YB3, D,J) NF-YC3 E,K) NF-YC4 F,L) NF-YC9. Scale bar in (A) equals 200 µm.</p

Multiple <i>cop1-4</i> mutant phenotypes are partially dependent on <i>NF-YC</i> genes.

<p>Partial suppression of <i>cop1</i> mutant phenotypes are quantified for <b>A)</b> dark-grown seedling hypocotyl elongation, <b>B)</b> rosette diameter, <b>C)</b> flowering time, and <b>D)</b> relative <i>FT</i> expression levels. Statistics and labeling as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006333#pgen.1006333.g002" target="_blank">Fig 2</a>, except <i>FT</i> expression statistics which were calculated using qBase software (Biogazelle).</p

NF-YC3, 4, and 9 are necessary for suppression of hypocotyl elongation in both cB and cR light.

<p>Hypocotyl lengths are shown for five day old plants grown on B5 media in <b>A)</b> cB (38μmol m^-2 s^-1), <b>B)</b> cFR (5μmol m^-2 s^-1), and <b>C)</b> cR (6μmol m^-2 s^-1). Statistically significant differences between groups (or lack thereof) are represented by lettering above bars (error bars represent 95% confidence intervals). Statistical differences were determined by standard ANOVA (p<0.01) when variances were not significantly different (cFR and cR) and Kruskal-Wallis ANOVA (non-parametric test, p<0.05) when variances were unequal (cB). Subsequent multiple comparisons were performed by either Tukey’s (cFR, cR) or Dunn’s (cB) procedures, respectively.</p