Extended Data Fig. 5: Dual functions of the basic domain of FD.

a, Multiple sequence alignment of group A bZIP proteins in Arabidopsis. Amino-acid residues conserved among all proteins are highlighted in red. Sequences can be found in Supplementary Table 1. b, Domain architecture of FD and alignment of the basic domain among group A bZIP proteins of Arabidopsis. c,d, Confocal images of shoot apical meristem cells of fd-3 plants expressing gFD::mVenus-FD wild-type (WT) or Mu1. The nuclei (magenta) were stained with DAPI. Scale bars = 20 μm. e, Quantification of nuclear signal intensity of mVenus-FD WT and mVenus-FD Mu1 proteins in shoot apical meristem cells from (c) and (d). Mann-Whitney U test was used to test whether the median of signal intensity of WT and Mu1 are different. Alpha value, WT vs. Mu1 = 0.00016. f, Flowering time (total leaf number, TLN) of transgenic fd-3 plants carrying gFD::3HA3Flag-FD Mu1. Different letters represent significant differences among genotypes (P < 0.05, using one-way ANOVA followed by Tukey’s pairwise multiple comparison, P = 1.11 * 10⁻¹⁶); n = 21 for gFD::3HA3Flag-FD Mu1, n = 12 for fd-3, and n = 11 for Col-0, respectively, all grown under long-days (LDs). g, RT-qPCR analysis of 2HA-mVenus-FD mRNA levels in shoot apices of transgenic fd-3 mutant plants carrying gFD::2HA-mVenus-FD^WTand gFD::2HA-mVenus-FD^Mu1. All values are normalized to ACTIN2 levels. Data are presented as mean values ± SEM of three biological replicates. Statistical significance was determined by pairwise one-sided t-test [P (FD^WT vs. FD^Mu1) = 0.001527. Shoot apices were harvested from seedlings grown for 7 LDs. h, Western blotting analysis of the abundance of 2HA-mVenus-FD proteins in total (left panel) and nuclear (right panel) extractions in 7 LD-grown seedlings. i, RT-qPCR analysis of 3HA-3Falg-FD mRNA levels in shoot apices of transgenic fd-3 mutant plants carrying gFD::3HA-3Flag-FD^WTand gFD::3HA-3Flag-FD^Mu1. All values are normalized to ACTIN2 levels. Data are presented as mean values ± SEM of three biological replicates. Statistical significance was determined by pairwise one-sided t-test [P (FD^WT vs. FD^Mu1) = 0.563. Shoot apices were harvested as described in (g). j, Western blotting analysis of the abundance of 3HA-3Falg-FD proteins in total (left panel) and nuclear (right panel) extractions in 7 LD-grown seedlings. k, Modeled structure of the FD^bZIP–DNA complex. k.1, Close-up of the predicted FD residues that interact with SEP3 DNA are colored by heteroatom. l, Windows for ChIP-seq analysis of the FD-binding profile to the SEP3 gene. The SEP3 DNA probes (28 bp) for EMSA experiments in (m) and Extended Data Fig. 4j are shown. m, Interactions between FD^bZIP WT and Mu1 proteins and DNA probes analyzed by EMSA (gel shift). Western blots in h,j are are representative of two independent experiments.