Fig. 2

Epigenome remodelling during medaka embryo development. (A) Heatmap of DNA methylation (mCG/CG) levels, ChIP-seq histone modification signal (H3K27me3, H3K4me3, H3K27ac) expressed as RPKM (reads per kilobase per million), ATAC-seq signal (RPKM), and CG density plotted over all developmental DMRs clustered into groups (k-means = 4). Embryonic stages assayed are: 32-cell, stage 8 early morula (st.8), stage 9 late morula (st.9), stage 10 early blastula (st.10), stage 11 late blastula (st.11), stage 24—16 somite (st.24), four days post fertilisation (4dpf), and gametes (sperm, egg). (B) Sub-clustering of cluster-4 DMRs based on mCG/CG levels (k-means = 2). (C) IGV browser snapshots of DNA methylation (mCG/CG) levels (upper panel), histone modification (H3K27me3, H3K4me3, H3K27ac), and ATAC-seq signal (RPKM) at developmental DMRs (blue boxes) during medaka development. Embryo drawings correspond to st.11 (pre-ZGA; upper drawing), and st.24 (16 somites – phylotypic period; lower drawing). Illustrations were adapted with permission from (34). (D) Average profiles of DNA methylation (mCG/CG) during medaka embryo development plotted over H3K27me3 peaks (st.11), ATAC-seq peaks merged from st.11, st.13, st.19, st.25, st.32, H3K4me3 peaks merged from st.11, st.24) and all H3K27ac peaks identified at st.11 and st.24 that do not overlap H3K4me3 peaks. Dotted lines represent sperm and pre-ZGA/ZGA samples whereas full lines denote egg and other embryonic stages.