Extended Data Fig. 6: Developmental 5mC dynamics at APREs in amphioxus.

a, k-means clustering (n = 2) of 5mC signal over embryo-specific open-chromatin regions (that is, APREs), assessed by ATAC-seq (Supplementary Table 10). b, The most significantly enriched transcription-factor binding-site motifs in APREs that display different developmental 5mC patterns in Fig. 2b. Uncorrected P values as provided by MEME. All plotted motifs had Benjamini-corrected q values of 0. c, GO enrichment for genes associated with cluster 1 (top) or cluster 2 (bottom) APREs from Fig. 2b. Uncorrected P values correspond to two-sided Fisher’s exact tests as calculated by topGO. d, Distribution of expression values (cRPKMs) across all samples for genes associated with cluster 1 (top, n = 1,114) or cluster 2 (bottom, n = 1,594) APREs from Fig. 2b. e, Distribution of the coefficients of variation for genes associated with cluster 1 or cluster 2 APREs from Fig. 2b, as well as all (n = 19,710), trans-dev (n = 357) and house-keeping (n = 862) amphioxus genes. f, Example of a potentially conserved (zebrafish to amphioxus) DMR associated with yap1, a major transcription factor of the Hippo pathway. The inset corresponds to the region highlighted in green. The two ohnologous genomic regions in zebrafish are shown in Supplementary Fig. 2. Additional cases included genes that contained APREs that are likely to regulate neighbouring liver-specific genes (‘bystander’ genes) (Supplementary Table 11). The number of replicates for each experiment displayed in each track is provided in Fig. 1a.