Extended Data Fig. 5: Mettl3-dependent m6A modification on H3K9me3-marked TEs.
From: The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity
a, Top, a schematic diagram showing the strategy of Mettl3 KO. Bottom, western blot validates the generation of the Mettl3-KO cell line. Immunoblotting was repeated at least three times with similar results. b, Metagene profiles of m6A signal along transcripts in two replicates for WT and Mettl3 KO mouse ES cells. c, Scatter plots showing the m6A level of m6A peak regions in WT and Mettl3 KO mouse ES cells. Hypermethylated peaks (green) and hypomethylated peaks (red) with m6A upon Mettl3 KO are shown. d, The overlap of m6A decreased TEs after Mettl3-KO from 4 independent studies. e, The m6A changes for TEs upon Mettl3 depletion from 4 independent studies. f, The m6A signal changes upon loss of Mettl3 in different studies for indicated TEs. Boxplots denote the medians and the interquartile ranges (IQR). The whiskers of a boxplot are the lowest datum still within 1.5 IQR of the lower quartile and the highest datum still within 1.5 IQR of the upper quartile. P values were from two-sided Student’s t-test. Data were from n ≥ 2 independent experiments. g, Read count tag density pileups of m6A RIP-seq reads for indicated TEs upon Mettl3 depletion from two independent studies. h, The overlap of Ythdc1 and Mettl3-dependent H3K9me3 marked TEs. P value is from one-tailed Fisher’s exact test. i, H3K9me3 level changes for Setdb1-dependent and -independent regions from Fig. 2e after Mettl3-KO (n = 2). P values are from two-sided Student’s t-test. Boxplots denote the medians and the interquartile ranges (IQR). The whiskers of a boxplot are the lowest datum still within 1.5 IQR of the lower quartile and the highest datum still within 1.5 IQR of the upper quartile. j, Tag density pileups of H3K9me3 ChIP-seq reads for indicated TEs upon Mettl3 depletion. k, Same as panel i, but for different TEs. l, Same as Fig. 3i, but only the unique mapped reads were kept. m, Tag density pileups of IAP (left) and LINE1 (right) ChIRP for indicated TEs upon Ythdc1-KO. n, Same as panel m, but for Mettl3-KO.
