Figure 1: Global features of DNA methylation across zebrafish embryogenesis.
From: Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos
(a) A schematic representation of the study. MeDIP-seq and MRE-seq libraries were constructed from genomic DNA of six developmental stages: sperm, 2.5, 3.5, 4.5, 6 and 24 hpf. Stage-specific drawings of representative embryos are adapted from ref. 26, with permission from Wiley-Liss, Inc., 1995. The two sequencing libraries for each developmental stage were further processed and analysed using recently developed algorithms, methylCRF and M&M. Both algorithms integrate MeDIP-seq and MRE-seq data. (b–d) The average DNA methylation level across different genomic features: gene-associated regions (b), CGIs and neighbouring regions (c), and high and low CpG density promoters (d). Promoter was defined as 1 kb upstream from TSS in b. CGI shore was defined as 2 kb regions flanking a CGI and CpG shelf as a 2 kb region outside a CpG shore (away from the CGI). The average CpG densities (grey lines) over the regions was also plotted in b and d.
