Figure 5.

Increased DNA methylation is observed at most N. crassa heterochromatin domains in H1-deficient strains. (A) The DNA methylation level (weighted DNA methylation level (%); (see Materials and Methods) is shown for 10 kb windows across N. crassa Linkage Group VII for wild-type, the $\Delta$hH1 mutant, and the $\Delta$dim-2 strain, which lacks all DNA methylation. (B–D) The metaplots show the average DNA methylation level across all previously identified wild-type methylated domains: (B) the wild-type mat A strain and the $\Delta$hH1 strain; (C) the wild-type mat a strain and the $\Delta$hH1 strain; and (D) the wildtype mat A strain and the hH1^RIP2 strain. Data for at least two independent biological replicates of each strain are shown. (E) More cytosines are methylated in $\Delta$hH1. The plot shows the total number of methylated cytosines (see Materials and Methods) identified in each wild-type and $\Delta$hH1 replicate. (F) The level of methylation at individual cytosines is higher in $\Delta$hH1. The percentage of total shared methylated sites (y-axis) vs. the level of methylation at individual cytosines (x-axis) is shown.