Extended Data Fig. 2: YTHDC2 occupies active genomic loci and limits transcriptional silencing of LTR7/HERV-H loci in hESCs.
a, Validation of YTHDC2 binding to LTR7 loci using Western blot. n = 3 biologically independent experiments. b, A permutation test was conducted to determine the enriched repeat families overlapping with YTHDC2 ChIP-seq peaks. Exact p values are in Supplementary Table 3,a. c, The indicated genomic datasets are presented as heatmaps centered on YTHDC2 ChIP-seq peaks. Each row represents one YTHDC2 peak. For all the heatmaps, the rows are sorted in the same order based on YTHDC2 ChIP-seq signal. d, Pie chart displaying the proportion of 15 chromatin states (defined by ChromHMM in H1 hESCs) in the YTHDC2 occupies DNA sequences. e, A permutation test was carried out in a similar way described in (b) to identify the enriched chromatin states in the YTHDC2-occupied DNAs. Exact p values are in Supplementary Table 3,b. f, YTHDC2 knock-out in the two mutant clones revealed by Western blot. g, h, YTHDC2 KO did not alter the expression of pluripotency markers at RNA (g) and protein (h) levels. KO no. 1, KO no. 2: two independent YTHDC2 KO clones. i, HERV-H RNA decay rate in the indicated hESCs. j, The protein expressions of wild-type and two mutant forms of YTHDC2 was restored in the YTHDC2 KO hESCs. n = 3 biologically independent experiments. k, l, HERV-H expression in control and mutant cells analyzed by RNA-seq are shown as boxplot (k) and volcano plot (l). P value determined by two-sided Wilcoxon signed-rank test. n = 2 biologically independent experiments. In the plots, center lines represent the median value, box limits the 25th and 75th percentiles, and whiskers denote minima and maxima (1.5× the interquartile range) (k). Blue and red dots: the downregulated or upregulated HERV-H RNAs in YTHDC2 KO compared to wild-type cells(l). Data represent mean ± s.e.m. from three experiments. ns, not significant; *p < 0.05, **p < 0.01, ***p < 0.001. P values were calculated by two-tailed Student′s test (g, i). Exact p values are in Source Data 1.
