Supplementary Figure 7: Both de novo methylation and demethylation are correlated with chromatin compartments. | Nature Genetics

Supplementary Figure 7: Both de novo methylation and demethylation are correlated with chromatin compartments.

From: Dynamic epigenomic landscapes during early lineage specification in mouse embryos

Supplementary Figure 7

a Barcharts showing the average methylation levels gained from E4.0 ICM to E5.5 Epi or E5.5 VE (left) in active gene bodies (+), inactive gene bodies (-), intergenic regions (i), and the whole compartment (w), for either compartment A or compartment B (left). b A chromosome-wide view of CH methylation levels (1Mb bin) is shown for E5.5 Epi and E5.5 VE (top). Chromatin compartments in E3.5 ICM, E6.5 Epi, E6.5 VE and gene-dense regions are also shown (bottom). Arrows indicate hypomethylated regions that overlap with compartment B. c Scatterplots comparing CG and CH methylation levels (1Mb bin) between epiblast and VE at E5.5 and E6.5. The Pearson correlation coefficients are indicated. d The average allelic methylation levels near active (green) or silenced (black) genes for E3.5 ICM are shown, before (top) or after (bottom) TAD-based normalization (subtracting TAD background methylation levels for each gene). The background methylation level for each TAD was calculated by averaging DNA methylation levels across the TAD (excluding gene bodies and regulatory elements such as promoters and putative enhancers). e Barcharts showing the average methylation differences between wild type and Tet3 knockout zygotes in active gene bodies, inactive gene bodies, intergenic regions and the whole compartment for either compartment A or B. f A chromosome-wide view of DNA methylation levels (1Mb bin) is shown for mESC (serum and 2i). Chromatin compartments and gene-dense regions are also shown

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