Methylation Trajectories in Different Genomic Contexts
(A) Distribution of methylation values at sequence features in sperm and the paternal component of control zygotes. The plot displays the median (bar), interquartile range (box), and maximum and minimum (whiskers). The p values shown are the result of a paired ANOVA multiple-comparison test with Sidak correction; “n” denotes the number of sequences that met quantification criteria.
(B) Absolute methylation change between sperm and the paternal component of control zygotes. Only changes ≥ 10% and significant according to a chi-square test (corrected p value < 0.05) are shown; all others are recorded as “no change.”
(C) RDL at identified demethylated loci, calculated by dividing the absolute paternal methylation change (as in B) by the sperm methylation level. Demethylated loci are defined as those that had an absolute paternal methylation loss of ≥10% and were significant according to a chi-square test (corrected p value < 0.05). n = 5,393 intergenic sequences, 7,405 gene body sequences, 4,213 CGI promoters, 1,366 non-CGI promoters, 526 promoter CGIs, and 257 nonpromoter CGIs.
(D) Distribution of early embryo paternal transcriptional noise levels at genes allocated into quartiles according to average intragenic methylation levels in the paternal pronucleus. Normalized transcriptional noise refers to expression-corrected variation in transcription from the paternal allele between single cells as calculated in . The p values shown are the result of an ANOVA multiple-comparison test between indicated data sets with Sidak correction. The differences between second and third quartiles, and third and fourth quartiles are not significant at any stage according to this test. The total number of genes that fell into each quartile was as follows: 0%–25%, 1,379; 25%–50%, 2,468; 50%–75%, 2,605; and 75%–100%, 270. Genes that were not expressed at a particular stage were excluded from analysis of that stage. The number of genes analyzed at each stage is given in .
(E) Relationship between the average paternal pronuclear gene body methylation and paternal transcriptional noise at the late 2-cell stage. A quadratic equation is a significantly better fit to the data than either a linear or no relationship (p < 0.0001 in both cases, extra sum-of-squares F test).
See also and .