Extended Data Fig. 6: YTHDC2 recruits TET1 to demethylate LTR7/HERV-H DNA.
a, Anti-V5 IP and western for TET1-V5 lines alongside parental, non-tagged WT cells. n = 3 biologically independent experiments. b, c, Comparison of the TET1-V5 ChIP-seq data generated in this study and in a prior study. The similarities of the two data sets were assessed by visualization of genome browser snapshot (b) and Pearson correlation(c). d, Protein co-immunoprecipitation experiments using lysates from cells transduced with indicated plasmids. n = 3 biologically independent experiments. e, Protein co-immunoprecipitation experiments using lysates treated with or without RNase. n = 3 biologically independent experiments. f, Protein co-immunoprecipitation experiments using lysates from cells treated with or without STM2457. n = 3 biologically independent experiments. g, YTHDC2 and TET1-V5 binding on LTR7s occupied by TET1-V5. h, Pearson correlation of YTHDC2 and TET1 ChIP-seq signals on co-occupied LTR7 loci. i, Volcano plot of RNA-seq data showing differentially expressed HERV-H transcripts in TET1 KO hESCs compared to the wild-type cells. The blue and red dots indicating substantially changed HERV-H RNAs (p-value < 0.05). j, ChIP-qPCR analysis of TET1 binding on the two LTR7 loci flanking the LINC-ROR in WT or YTHDC2 KO cells upon m6A editing. k, l, MeDIP-qPCR analyses of the two LTR7 loci flanking the LINC-ROR locus using antibodies against 5mC (k) or 5hmC (l). In the box plots (j-l), center lines represent the median value, box limits the 25th and 75th percentiles, and whiskers denote minima and maxima (1.5× the interquartile range) n = 3 biologically independent experiments. ns, not significant; *p < 0.05, **p < 0.01, ***p < 0.001. P values were calculated by two-tailed Student′s test in (j-l). Exact p values are in Source Data 1.
