Fig. 1

The lncRNA APOLO and the methylcytosine-binding protein VIM1 are thermomorphogenesis regulators. A Chromatin isolation by RNA purification (ChIRP)-Dot blot analysis of APOLO interaction with GFP-VIM1. ChIRP was performed using ODD and EVEN sets of probes against APOLO or using LacZ probes as a negative control. Dot blots are revealed with an anti-GFP antibody and an HRP-conjugated secondary antibody. Diluted INPUT (*1/50) were used as loading control. B RNA immunoprecipitation (RIP) assay in Nicotiana benthamiana leaves transiently co-transformed with APOLO and GFP-VIM1 translational fusion expressed under the control of the 35S-CaMV promoter, or in Arabidopsis thaliana 2-week-old VIM1 over-expression (OE VIM1-1) seedlings. Results are expressed as a percentage of the INPUT fraction. Anti-IgG antibodies were used as a negative control, and the asterisks indicate Student’s t test ≤ 0.05 (n = 3) between anti-GFP and anti-IgG RIPs. The non-specific background level of RNA precipitation (PP2A) is also shown in Arabidopsis. C Fold change of APOLO and VIM1 expression levels in relation to 23 °C control conditions in 4-day-old wild-type (WT) seedlings treated with heat (29 °C) for 6 h. Asterisks indicate Student’s t test ≤ 0.05 (n = 3) for levels of each corresponding gene between 23 and 29 °C. D, E Boxplots showing hypocotyl length quantification ratio at 29 °C over 23 °C of 4-day-old OE APOLO-1, OE APOLO-2 (D) or vim1-2, vim1-3 (E) seedlings and their associated WT. Values are represented by colored points. F Venn diagram of differentially expressed transcripts in WT treated with heat (29 °C) for 6 h, and in untreated OE APOLO-1 and vim1-3 seedlings. G Heatmap showing log₂(fold change) compared to WT 23 °C. A correlation of up- and downregulated genes in WT in response to 29 °C is observed for OE APOLO-1 and vim1-3 at 23 °C. H Gene Ontology (GO) enrichment analysis of upregulated transcripts in WT treated with heat. Top ten GO categories with more significant p-values are shown. Violet bars: auxin-related pathways. The ShinyGO Browser is located at bioinformatics.sdstate.edu and published in [54]. In A, each sample was serially diluted as indicated in the plot, and two additional biological replicates are shown in Additional file 1: Fig. S1A. In B, bars represent average ± SD (n = 3 biological replicates). In C, transcript levels are normalized relatively to the untreated control to show fold changes. Bars represent average ± SD (n = 3 biological replicates). In D, E, results are the mean of three biological replicates and letters indicate significant differences compared to WT, based on a Kruskal-Wallis test (α = 0.05; n ≥ 134)