Extended Data Fig. 3: METTL3 is required for heterochromatin formation.
From: METTL3 regulates heterochromatin in mouse embryonic stem cells
a, Box plots showing enrichment levels of H3.3 on IAPEz-int elements (n = 2,542) in parental, Mettl3 KO and rescued cell lines with METTL3WT or METTL3APPA. ****P < 0.0001 (exact P values from left to right: 4.2 × 10−218, 2.7 × 10−274, 3.9 × 10−294), two-sided paired t-test. b, Box plots showing CpG methylation ratios on IAPEz-int elements (n = 2,542) in parental, Mettl3 KO and rescued cell lines with with METTL3WT or METTL3APPA. ****P < 0.0001 (exact P values from left to right: 4.87 × 10−111, 1.5 × 10−150, 0), two-sided paired t-test. c, Box plot showing density fold changes (log2[Mettl3 KO/parental]) of H3.3 on different types of repetitive elements upon Mettl3 KO. d, Box plot showing CpG methylation changes on different types of repetitive elements upon Mettl3 KO. Only elements with at least ten covered CpGs were used. e, RT–qPCR showing RNA levels of IAPEz-int in parental, Mettl3 KO and rescued cell lines with METTL3WT or METTL3APPA. The mean of three replicates ± s.d. is shown. *P < 0.05, **P < 0.01, two-sided t-test. Exact P values are provided in the Source Data. f, Box plot showing density fold changes (log2[Mettl3 KO/parental]) of RNAs of different types of repetitive elements upon Mettl3 KO. g–j, Scatter plots showing correlation between METTL3 (g), H3K9me3 (h), H4K20me3 (i), DNA methylation (j) and RNA expression level on IAPEz-int (n = 2,542). Two-sided Pearson’s correlation test. k, Box plot showing RNA levels of IAPEz-int (n = 2,542) in parental, Mettl3 KO and Ythdf1/2/3 KO cell lines revealed by PolyA RNA-seq (GSE147849). ****P < 0.0001 (exact P values from left to right: 1.1 × 10−52, 7.3 × 10−37), two-sided paired t-test. Uniquely mapped ChIP–seq reads were used in a–d, f–k. For the box plots in a–d, f and k, the middle line and lower and upper hinges of the box plot correspond to the median and the first and third quartiles, respectively. The whiskers extend from the hinges to no further than 1.5 × IQR from the hinge. Outlying points are plotted individually.
