Figure 1. Human preimplantation embryos are globally hypomethylated.
a. Top. DNA methylation across 100 bp tiles for human sperm, preimplantation embryos, including the ICM and TE, ESC derivation from outgrowth to 5th passage, and somatic fetal tissues representing all germ layers. Gray highlights the average. Bottom. Boxplots of methylationat different local CpG densities. Bulls-eye signifies the median, boxes and lines the 25th/75th and 2.5th/97.5th percentiles, respectively.
b. Bar plots of 100 bp tiles segregated by non-repetitive (unique) or repetitive designation and binned by methylation status. Sp, sperm; Cl, cleavage; Bl, blastocyst;Som, somatic. “ESC” and “Som” refer to the average of these timepoints.
c. Non-repetitive 100 bp tiles are clustered via k-means into 10 dynamics. Sperm hypermethylated sequences follow three general trajectories: persistent maintenance, incomplete or complete demethylation. Other dynamics include sperm specific hypermethylation and sperm/early embryonic hypomethylation that is de novo methylated in ESCs. Finally, 3,586 tiles are hypomethylated in sperm and ESCs but methylated in embryos, representing transient imprint-like signatures.
d. Dynamics for sperm hypermethylated, non-repetitive tiles as clustered in (c). Left heatmap, per cluster average of tiles. Right heatmap, –log10 p value of hypergeometric enrichment for each cluster for intergenic, exonic, intronic, CGI, or TSS annotations using sperm hypermethylated regions as the background.
e. Violin plot forsperm hypermethylated intergenic (inter), exonic, and intronic features.
f. The OBSCN gene exhibits high inter- and intra-genic methylation and an unmethylated promoter in sperm and ESCs. In cleavage embryos, a 130 kb region, highlighted in blue, remains specifically methylated while the periphery is demethylated.