Fig 2: PIF4 acts downstream of TZP in red light signaling. Hypocotyl measurements of mutant combinations between tzp and pif4, pif4 pif5 and controls. Seedlings were grown for 5 days in red light (1 µmol m-2 s-1). Hypocotyl lengths (A) and graphs of representative images (B) of Col-0, tzp, pif4, tzp pif4 1.29.4, tzp pif4 1.20.5, pif4 pif5, tzp pif4 pif5 2.2.3, tzp pif4 pif5 1.20.4, phyB seedlings grown in the indicated conditions. tzp pif4 1.29.4, tzp pif4 1.20.5 are two independent tzp pif4 double mutant lines; tzp pif4 pif5 2.2.3, tzp pif4 pif5 1.20.4 are two independent tzp pif4 pif5 triple mutant lines. Scale bar, 3 mm. Seedlings were scanned at the end of the fifth day. Hypocotyl length was measured from digital images using ImageJ. In whisker plots, boxes show median, IQR, and maximum–minimum interval of each data set (n = 15 seedlings). Data shown are representative of three biological replicates with independent populations of seedlings. Different lowercase letters represent significant differences by one-way ANOVA with Tukey’s post hoc test among assessed samples (P < 0.05).

Fig 3: SlPIF4 promotes the gene expression and endogenous levels of ABA and JA biosynthesis in response to cold stress. (a) and (c) Expression of NCED6 (a) and AOS2 (c) in tomato WT, pif4 mutant and SlPIF4-OE plants after exposure to 25 °C or 4 °C under low R/FR (L-R/FR, 0.5) light conditions for 6 h. (b) and (d) Endogenous levels of ABA (b) and JA (d) biosynthesis in tomato WT, pif4 mutant and SlPIF4-OE plants after exposure to 25 °C or 4 °C under L-R/FR light for 12 h. For light-quality treatments, plants were maintained at R conditions (120 µmol m-2 s-1) and supplemented with different intensities of FR. Data are presented as the means of three biological replicates (±SD). Different letters indicate significant differences (P < 0.05) according to Tukey’s test.

Fig 4: SHB1 and CCA1/LHY are associated with the PIF4 promoter. a PIF4 promoter demonstrating the chromatin regions (4–1, 4–2, 4–3, and 4–4) used for ChIP-quantitative PCR analysis and the potential Myb-binding sites M1 and M2 (asterisks). Association of SHB1:GFP b and CCA1:FLAG or SHB1:GFP in cca1 lhy c with the PIF4 promoter. d Rhythmic association of CCA1, LHY, or SHB1:GFP with the PIF4 promoter under 12-hr dark and 12-hr red light cycles from two biological replicates. Enrichment of DNA fragments was quantified by qPCR and normalized to that of UBQ10. e Rhythmic PIF4 expression at various ZT points in Ws and 35 S::SHB1:GFP transgenic plants under 12-hr dark and 12-hr red light cycles. Data are presented as the means ± SE calculated from two biological replicates. Source data are provided as a Source Data file

Fig 5: CCA1/LHY and SHB1 enhance PIF4 expression and thermomorphogenesis. Hypocotyl lengths of Col, shb1, Ws, pif4, shb1-D, and shb1-D pif4 a; Ws, cca1, lhy, and cca1 lhy b; three 35 S::PIF4:GFP lines in Ws or cca1 lhy c; and Ws, shb1-D, cca1 lhy, and shb1-D cca1 lhy d, e under 30 µmol m-2 s-1 white light at 20 °C for 7 days or 20 °C for 4 days followed by 29 °C for 3 days. Bar = 5 mm. Significance levels by Student’s two-tailed heteroscedastic t tests in a: p < 0.001 between a and b, c and d, c and e, c and f, d and e, or e and f and p < 0.01 between d and f; in b: p < 0.001 between a and b; in c: p < 0.001 between a and b or c and d; in d: p < 0.001 between a and b, a and c or b and c. f PIF4 expression in Col, shb1, Ws, shb1-D, cca1 lhy, and shb1-D cca1 lhy. Seedlings were grown at 20 °C for 5 days and then incubated at 20 °C or 29 °C for 4 h. PIF4 expression in each sample was normalized to that of UBQ10, and data are presented as the means ± SE. Source data are provided as a Source Data file