Fig. 2: BMAL1 facilitates binding of TRIM28, H3K9me3 labelling, and transcriptional repression of MERVL elements in mESCs.

A Genomic distribution of TRIM28 binding peaks. B Heatmap comparing TRIM28 binding signal (calibrated reads) in JM8^+/+ and Bmal1^-/- mESCs around the centre of regions bound by TRIM28 in JM8^+/+ cells and classified in indicated categories. C Volcano plot showing the expression level of individual TEs in Bmal1^-/- relative to JM8^+/+ mESCs. Significantly upregulated (FC > 2, p < 0.05, red colour), downregulated (FC < 2, p < 0.05, blue colour) or unchanged (grey colour) TEs are shown. p-values were calculated by Wald test with Benjamini-Hochberg correction. (D) Pie chart showing the classification of the 1730 TEs that are overexpressed in Bmal1^-/- mESCs. E Top panel shows a bar plot displaying the subfamily classification of the 1730 TEs that are overexpressed in Bmal1^-/- mESCs. Bottom panel is a violin plot showing the median upregulation (log₂ fold change expression of Bmal1^-/- versus Jm8^+/+) of individual TEs grouped by subfamily. F Heatmap showing the reduction of TRIM28 and H3K9me3 enrichment (as assayed by cChIP-seq) and the increase in mRNA expression (measured by mRNA-seq) in Bmal1^-/- relative to JM8^+/+ at the consensus sequence of indicated families of TEs. G Plots displaying the TRIM28 and H3K9me3 enrichment signals along the consensus sequence of full MERVL (left panels) or MERVL-specific LTR (also known as MT2_mm) elements (right panels) in JM8^+/+ and Bmal1^-/- mESCs. p-values calculated by two-way ANOVA. H Plots displaying the average BMAL1, TRIM28 and H3K9me3 enrichment profile along the genomic regions containing the full length MERVL (as previously defined⁸⁶, n = 594) (top panel) or IAPEz copies (longer than 5Kb, n = 841) (bottom panel). p-values calculated by a two-way ANOVA. Source data are provided as a Source Data file.