Fig. 2: Combined csRNA-seq and ATAC-seq analysis reveals dynamics of gene regulatory programs and non-coding transcription during the seed-to-seedling transition.

a Heatmap of developmental clusters from the csRNA-seq time-series. Rows represent Z-scores of the expression of individually annotated TSSs. Associated genes were enriched for overrepresented gene ontology terms, followed by an individual keyword enrichment analysis to generate word clouds of overrepresented keywords to the right of the heatmap, with their size being proportional to the level of enrichment. b Heatmap of developmental clusters from the ATAC-seq time-series. Rows represent Z-scores of the accessibility of individual ACRs. A word cloud of enriched keywords from a gene ontology enrichment analysis for ACR-associated genes is shown on the right. c Comparison analyses of the csRNA-seq and ATAC-seq clusters. The left heatmap shows the Pearson correlation coefficient between the average Z-score profiles of each cluster. The right heatmap shows the Jaccard coefficient of the number of common associated genes of each cluster. Comparisons with significant overlap are marked with an asterisk (P-value < 10⁻⁶). Significance testing was performed using Fisher’s exact test without correction for multiple testing. d Proportion of annotated TSS types in the csRNA-seq clusters. e Proportion of annotated ACR types in the ATAC-seq clusters.