Fig. 4

Complete loss of DNA methylation causes extensive conversions of histone modifications. a Overlap of histone modifications in mddcc and the wild type. b Conversion patterns of histone modifications between mddcc and the wild type. c Examples of histone modification conversions. d Histone modification conversion model. The line thickness is proportional to the switching frequency. e Composition (emission probability) of six histone modifications and RNA polymerase II (RNAPII) occupancy, and ratio of the observed probability that a region switches from one chromatin state (row, the wild type) to another (column, mddcc). f Properties of chromatin states defined in mddcc and the wild type. Red and yellow asterisks indicate higher and lower enrichments in mddcc than in the wild type, respectively. Black asterisks indicate a significant difference in the expression of TEs in the same chromatin state between mddcc and the wild type. *p < 0.001 from Wilcoxon test. g Peak intensity and DNA methylation of the indicated categories in (a and b)