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Fig. 1 | Zoological Letters

Fig. 1

From: Recapitulation-like developmental transitions of chromatin accessibility in vertebrates

Fig. 1

Strategy for assessing accessible chromatin landscapes in vertebrate embryos. a Genome browser views showing enrichment of whole-embryo ATAC-seq reads in representative regions of mouse, chicken, and medaka genomes, respectively. ATAC-seq read enrichment is presented as the mean of three biological replicates. Colors below the read enrichment represent the estimated evolutionary ages of genomic regions that correspond to the tracks of the evolutionary trajectories, which are shown as a phylogenetic tree on the right. b The representative ACRs (blue boxes) overlapping with annotated enhancers (red regions) acquired from the VISTA Enhancer Database [23]. For each enhancer, ATAC-seq read enrichment in E10.5 and E12.5 mice and in vivo enhancer activity in E11.5 mice are shown with the VISTA Enhancer ID, the flanking gene, and an embryo image from the VISTA Enhancer Database [23]. c Schematic diagram showing the three steps for estimating the relative ATAC-seq signal for each evolutionary age: (1) ACRs were identified by ATAC-seq signal intensity; (2) ACRs were categorized according to their estimated evolutionary ages; and (3) for each developmental stage, the percentage corresponding to the summed signal intensities of each evolutionary category divided by the total signal intensities for all evolutionary categories was calculated (relative ATAC-seq signals)

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