Extended Data Fig. 2: Impact of LIF–Stat3 and Dnmt3a/b on genome methylation.

a, MeDIP-qPCR of repetitive elements in S3+/+ and S3-/- cells. Mock immunoprecipitations with a non-specific IgG antibody served as negative controls. Mean of 2 experiments, shown as dots. b, Volcano plot showing the significant differentially methylated CpG sites (q-value < 0.01, difference > 10% or < 10%) between S3+/+ 2i and S3+/+ 2iLIF cells, out of 1,327,475 detected sites. c, d Scatter plot showing the mutual changes in expression and DNA methylation at active promoters (c) and enhancers (d) between S3+/+ 2i and S3+/+ 2iLIF cells. Red dots: genes for which both changes were statistically significant (q-value < 0.01). e, Scatter plot comparing effects on transcription of the absence of LIF (S3+/+ 2i) and the absence of Stat3 (S3-/- 2iLIF). Pearson’s correlation coefficient (R) and corresponding p-value are indicated in the panel. f, Volcano plot showing the significant differentially methylated CpG sites (q-value < 0.01, difference > 10% or < -10%) between E14 2i and E14 2iLIF cells, out of 1,084,350 detected sites. g, CpG methylation changes caused by LIF addition (y axis) or by Dnmt3a/b deletion (x axis, Dnmt3a/b dKO.1). Dots indicate all CpG sites covered (sequencing depth >10x) in at least one technical replicate of each sample; blue dots: hypomethylated sites (q-value < 0.01, difference < -10 %). h, Volcano plot showing the significant differentially methylated CpG sites between Dnmt3a/b dKO.1 and E14 cells cultivated in 2i.i, CpG methylation changes caused by LIF (y axis) or by Dnmt3a/b deletion (x axis, Dnmt3a/b dKO.2), as described in panel g. j, Volcano plot showing the significant differentially methylated CpG sites between Dnmt3a/b dKO.2 and E14 cells cultivated in 2i. k, Venn diagram of CpG sites whose methylation status is dependent on either LIF (light blue) or Dnmt3a/b (red) or on both (grey intersection), for an independent mutant Dnmt3a/b dKO clone (Dnmt3a/b dKO.2).

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