Fig. 4. Genome-wide methylation analyses via ONT sequencing.
a CpG methylation ascertained by ONT sequencing of MEFs (brown), control miPSCs (CTRL, green), and miPSCs derived in the presence of lamivudine (3TC, pink). Results are shown for the whole genome (10kbp windows), the proximal promoters (−1000, +500) of protein-coding genes119, the 5′UTR of TF, GF, and A-type L1s > 6kbp, B1 and B2 SINEs, and MERVL MT2 and IAP long terminal repeats. Note: the 6 control and 3TC-treated miPSC replicates are displayed in aggregate to compare against the single MEF replicate, and the number of elements in each category is shown underneath. Box plots indicate the median, interquartile range, and 1.5× interquartile range. b Composite L1 TF methylation profiles. Each graph displays 100 profiles. A schematic of the TF consensus is provided at top. Average values are indicated by more thickly colored lines. c, Methylation profile of the Fsd1l locus obtained by ONT sequencing. The first panel shows an L1 TF orientated in a sense to intron 6 of Fsd1l, as well as an expressed sequence tag (EST) obtained from a mouse ESC sample and supporting a transcript initiated in the TF 5ʹUTR and spliced into a downstream Fsd1l exon. The second panel displays ONT read alignments, with unmethylated CpGs colored in brown (MEFs), green (control miPSCs) and pink (3TC-treated miPSCs), methylated CpGs colored black, and CpGs not confidently called, i.e. abs(log-likelihood ratio) > 2.5, omitted. The displayed miPSC data were downsampled to the approximate depth of the MEF data with Picard DownsampleSam version 2.27.4. The third panel indicates the relationship between CpG positions in genome space and CpG space, including those corresponding to the TF 5ʹUTR (shaded light blue). The fourth panel indicates the fraction of methylated CpGs. Note: this L1 TF is polymorphic amongst inbred mouse strains56. Source data are provided as a Source Data file.