Extended Data Fig. 3: Generation of Uhrf1 KO TKOL clones and enrichment of H3K9me3 at DMRs.
From: Dnmt1 has de novo activity targeted to transposable elements
a, Amplicon hairpin-bisulfite sequencing data for several repeat classes in WT, TKOL, P1, and P5 DKO0 with columns representing covered CpGs, except the leftmost (average) and rows individual reads. Light blue represents an unmethylated CpG dyad, orange a fully methylated one, and dark and light green represent plus or minus-strand hemimethylation. b, The same amplicon data from panel a depicted as log2 fold-change of all CpG dyad combinations for WT, P1, and P5 DKO0 CpG versus TKOL. c, Correlation of DNA methylation rates in WT measured by WGBS and Nanopore at CpG resolution and over 1kb windows. d, DNA methylation distribution based on Nanopore sequencing. Shown are mean methylation levels of DMRs (left n = 1,335) and CRs (right, n = 1,268,188) in WT, TKOL, and DKO0 ESC. For violin plots, white dots indicate the median, the boxes indicate first and third quartiles; whiskers, 1.5 x inter-quartile range; data beyond the end of the whiskers are omitted. e, Comparison of mean DMR methylation levels of TKOL vs. DKO0 cells and mean CR methylation levels of TKOL vs. DKO0 cells. f, Comparison of WGBS and Nanopore methylation levels. DMRs with a difference below 0.05 (Nanopore), were discarded. Gray dots represent unsupported, filtered DMRs with a mean difference of less than 0.05 (n = 1,058). g, Methylation distribution (WGBS) of supported (remaining) and unsupported (excluded) DMRs (n = 1,515 and 1,058, respectively). For violin plots, white dots indicate the median, the boxes indicate first and third quartiles; whiskers, 1.5 x inter-quartile range; data beyond the end of the whiskers are omitted. h, Fraction of Nanopore single-read methylation levels in DMRs with at least 5 CpGs and spanning a minimum of 80% of the DMRs for WT, TKOL and DKO0.
