Extended Data Fig. 4: Motif activity analysis.

MARA predicts up-regulation of Tead3’s activity from gastrulation onwards (Fig. 2). For each potential target promoter with Tead3 binding site, MARA quantifies the extent the Tead3 motif activity explains the target’s expression dynamics (log-likelihood score). For each GO category the sum of log-likelihoods for all genes in the category was calculated. Supplementary Table 13 shows the GO biological process categories with the highest total log-likelihoods. Top categories correspond to processes in which Hippo signalling during early development in zebrafish has been implicated. a,b, The tgif1 promoters are transiently upregulated during gastrulation (a) while the targets of Tgif1 are transiently down-regulated (b), supporting Tgif1 as a repressor. Posterior means and standard deviations (depicted as error bars) are based on analysis of the expression levels of all n= 27781 promoters for each sample. c, Scatterplot of TGIF1_MEIS1a_MEIS2a motif activity (horizontal axis) against total tgif1 mRNA expression (vertical axis) shows motif activity and TF expression are highly anti-correlated (Pearson correlation -0.92). d, Scatterplot of the FOS/NF-Y motif activity (horizontal axis) against expression of the nfyal gene shows positive correlation (Pearson correlation coefficient 0.86). e, Scatterplot of the FOS/NF-Y motif activity (horizontal axis) against expression of the nfya gene shows negative correlation (Pearson correlation -0.77). As shown in Fig. 3d, MARA predicts that targets of NF-Y are down-regulated from the sphere stage onwards, thus as the NF-Y motif activity decreases during development. The expression of nfya is up whereas nfyal is down-regulated, suggesting that Nfya may replace Nfyal in the NF-Y complex. f, STRING database network picture of the predicted target genes of the NF-Y motif. The black oval indicates a set of target genes involved in mitosis and G2/M transition, consistent with the documented role of NF-Y.