Fig. 2: SPL/NZZ direct target genes are shared with MADS-domain TFs.

A Bar plot showing the SPL/NZZ ChIP-seq peaks localisation along the genome. Around 80% of the identified peaks fall within transcriptional regulatory sequences, such as promoters, 5′ UTRs, first exons, first introns, and 3′ UTRs. The experiment has been performed on three biological replicates of SPL/NZZ:GFP AP1:GR ap1cal inflorescences at 9 DAI. Peaks were considered significant with FE > 0, FDR ≤ 0.05 and if present in at least 2 biological replicates out of 3. The full list of SPL/NZZ targets identified by ChIP-seq can be found in Supplementary Data 2. B The CArG-box motif is the only enriched TF DNA sequence binding-site identified among the SPL/NZZ ChIP-seq peaks. The analysis has been performed with the XTREME tool from the MEME suite. C Venn diagram showing the intersection between the SPL/NZZ ChIP-seq peaks and the SEP3 ChIP-seq peaks. 185 SPL/NZZ peaks, representing more than 90% of the total peaks, are overlapping with SEP3 peaks. D SPL/NZZ ChIP-seq and SEP3 ChIP-seq overlapping peaks visualisation along the A. thaliana genome. All the significant SPL/NZZ ChIP-seq peaks are visualized in green. SEP3 ChIP-seq peaks overlapping with SPL/NZZ ones are shown in magenta. The full list of SPL/NZZ-SEP3 common targets can be found in Supplementary Data 2. E wild type, spl-1 and pSPL/NZZ::MADSas ovules at stage 2-IV. Even if with a milder effect with respect to the spl-1 case, pSPL/NZZ::MADSas fails in the differentiation of the MMC, that could be clearly identified in the wild type nucellus. F Bar plot showing the mean ± SEM of the percentage of ovules developing the MMC in wild type, spl-1, pSPL/NZZ::MADSas L1 (shp1,2,STK/STK), pSPL/NZZ::MADSas L2 (shp1,2,STK/STK) and pSPL/NZZ::MADSas L3 (shp1,2,stk). The analysis has been performed on 5, 5, 5, 9 and 4 different pistils, respectively, for the wild type (122 ovules observed in total), spl-1 (110 ovules observed in total), pSPL/NZZ::MADSas L1 (113 ovules observed in total), pSPL/NZZ::MADSas L2 (208 ovules observed in total), pSPL/NZZ::MADSas L3 (67 ovules observed in total). Source data are provided as a Source Data file. Letters above the bars indicate homogenous categories with p ≤ 0.05 as determined by one-way ANOVA with post-hoc Tukey HSD test. Exact P values for each comparison can be found in the Source Data file. Single measures are represented with dots in the bars. nu nucellus, fu funiculus, ii inner integument, oi outer integument, in integument, MMC megaspore mother cell. Scale bar = 20 µm.