Extended Data Fig. 6: TASOR or MPP8 deletion reduced H3K9me3 eSPAN bias in mES cells, while having little effects on H3K9me3 levels.

a. Immunoblots to confirm the knockout of MPP8 and TASOR in mES cells. Note that ORF1p were markedly up-regulated, while total H3K9me3 levels didn’t change to a detectable degree. n = 3. b, c. H3K9me3 CUT&Tag signals at HO L1s in Mpp8 KO (b) and Tasor KO (c) mES cells, compared to WT cells. Two repeats for each mutant were shown in the heatmaps (top), with the average H3K9me3 density shown at the bottom. Heatmaps were sorted by the average H3K9me3 signals of each row in WT cells. The relative position of a full-length L1 was shown in blue. d, e. H3K9me3 CUT&Tag signals at HO L1s in Mpp8 KO (b) and Tasor KO (c) mES cells, compared to WT cells. Two repeats for each mutant were shown in the heatmaps (top, sorted as in b), with average density shown at the bottom. L1s with reduced H3K9me3 levels for more than 1.5-fold were grouped as Down and those without significant changes were grouped as no-difference (No-diff). Note that less than 130 (~1%) L1s showed significant reduction of H3K9me3 density. f. Snapshots of H3K9me3 CUT&Tag signals and eSPAN bias in WT, Mpp8 KO and Tasor KO mES cells at three loci. Note that H3K9me3 CUT&Tag in Mpp8 KO and Tasor KO were performed in separate batches with their corresponding H3K9me3 CUT&Tag in WT cells (WT1 and WT2 shown for more accurate comparisons. g. Box plots of H3K9me3 eSPAN bias at two groups of HO L1s (n = 12,679) in WT, Mpp8 KO (left) and Tasor KO (right) mES cells. An average of two independent repeats were shown and L1s were grouped as in d, e. Box plots (g) show the median, 25% and 75% quartiles and minimal and maximal values with p values by two-sided Mann–Whitney–Wilcoxon tests, and Bonferroni correction for multiple comparisons. Each panel is a representative of at least two independent experiments. See Materials and Methods for more details. For gel source data, see Supplementary Fig. 1.

Source Data