Skip to main content
. Author manuscript; available in PMC: 2014 May 22.
Published in final edited form as: Cell. 2013 May 9;153(4):759–772. doi: 10.1016/j.cell.2013.04.030

Figure 3. Maternal DMRs Resolve to Resemble Paternal Status by Sphere Stage.

Figure 3

(A) Pairwise comparisons between developmental stages (summed) yielded differentially methylated regions (DMRs, 500 bp windows, ≥5 CpG, ≥5 reads per C; criteria, FDR R 0.001 and absolute log2Ratio ≥ 1.5, >20% change in fraction methylation). Combined unique regions were scored for mean fraction CG methylation across developmental stages and clustered (k-means, k = 9).(B) DMR locations were intersected with annotations (Ensembl). (C) Obs/exp frequency was calculated for each DMR cluster from (A). (D) DNAme reprogramming of the maternal genome occurs in maternal haploids. Assessment of whether DNAme reprogramming in early embryos relies on the continued presence of the paternal genome. The experimental setup (left) compares two types of sphere-stage embryos: (1) maternal/paternal diploid embryos derived from IVF (top) of wild-type oocytes and sperm containing a known mutation in the golden allele (gol b1, marking the paternal genome, yellow color), and (2) maternal haploid embryos derived from IVF of wild-type oocytes and UV-treated (yellow bolt, bottom) sperm from golden males, providing extensive DNA damage and rendering the genome incompetent for replication, rendering a sphere-stage embryo with only maternal DNA (red nucleus in outset). DNA was isolated from sphere-stage IVF embryos, and DNAme levels (mean fraction CG methylation) were assessed at each of 15 promoter regions (krt4, krt8, dnmt6, rarga, zgc:92231, zgc:101640, cpn1 hoxb1a, hoxb3a, pou5f1, dazl, vasa, irx3a, ntl, and dnmt3) using bisulfite sequencing of promoter amplicons in a high-throughput format (right). Here, the order of the genes at right (top to bottom) aligns with the order of the bars in the figure (left to right). Promoters representing sperm DMRs are depicted in red, and oocyte DMRs are depicted in blue. For comparisons, DNAme levels (mean fraction CG methylation) of these same 15 promoters from sperm, oocytes, and normal diploid sphere-stage embryos (converted from our genome-wide data) are provided.

See also Figures 4, S6, and S7 and Tables S4 and S7.