Fig. 3.

Characteristics of HMCs in Mili^−/− brain. (A) Enrichment analyses of HMCs within various annotation categories. The relative abundance of each annotation category within HMCs was compared with that over all consensus CpGs in Mili^−/− brain tissues. Statistical significance was determined by Permutation test, n = 1,000 (refer to SI Materials and Methods for detail). (B) Distribution of HMCs along copies of LINE1 in Mili^−/− brain tissues. Each circle represents individual HMC plotted over its distance from LINE1 transcription start site (TSS) vs. differential methylation. n = 3 per tissue per genotype. The dotted line separated HP from PFC, showing greater hypomethylation in mutant HP. Retrotr., retrotransposon.