Extended Data Fig. 5: Global DNA methylation analysis by enzymatic methyl sequencing (EM-seq).
From: Disruption of TAD hierarchy promotes LTR co-option in cancer
a,b, Representative distribution plots of DNA methylation sequencing coverage (a) and global DNA methylation levels (b) with NIPBL perturbation (shNIPBL_1 and shNIPBL_2) and control (shLuc). n = 2 biological replicates. c,d, Representative DNA methylation density plots under shLuc condition for baseline CTSSs and differentially regulated CTSSs by shNIPBL_1 (c) and shNIPBL_2 (d) perturbations. e,f, Histogram of CpG methylated regions under shLuc condition for baseline CTSSs and differentially regulated CTSSs by shNIPBL_1 (e) and shNIPBL_2 (f). g,h, Scatter plots showing differential methylation β vs. log2(fold change) of CTSS in shNIPBL_1 (g) and shNIPBL_2 (h) conditions. i–m, Representative DNA methylation profiles by EM-seq of significantly upregulated CTSSs in ALK intron 19 altP region (i), ULK4 (intron 31; j), LINC01387 (intron 2; k), between SYN3 and LINC01640 (intergenic regions; l) and between TAS2R39 and TAS2R40 (intergenic regions; m). Coverage (Cov) and methylation conversion (methyl) tracks were shown.
