Extended Data Fig. 5: DMRs show enrichment of UHRF1 and TRIM28.
From: Dnmt1 has de novo activity targeted to transposable elements
a, Western blot confirming the FLAG tagged version of the endogenous Uhrf1. FLAG tag was recognized with an anti-FLAG antibody, with signal only observed in targeted cell lines. The UHRF1 blot shows the expected increase in the size of the UHRF1-FLAG protein and demonstrates comparable expression to non-FLAG tagged controls. n = 1. b, Heatmap of UHRF1 enrichment at DMRs. ChIPmentation-seq of FLAG-tagged Uhrf1 shows enrichment at DMRs for all replicates from WT, TKOL, and DKO0 ESCs. The signal is displayed as fragment pile up per million reads per replicate. c, Volcano plot of interacting proteins acquired by Rapid Immunoprecipitation Mass Spectrometry (endogenous protein purification mass spectrometry) for TKOL and DKO0 cells with endogenous Uhrf1-FLAG used as bait. Uhrf1-FLAG immunoprecipitation shows enrichment for known interactors like Lig1, heterochromatin, and DNA methylation associated proteins in both cell lines. Zoom highlights enriched proteins (see Supplementary Table 3). d, Visualization of a gene set enrichment analysis for TKOL and DKO0 for Uhrf1 interacting proteins as detected by Rapid Immunoprecipitation Mass Spectrometry. Significant enrichment for heterochromatin and condensed chromatin as well as for methyltransferase complexes was found for the DKO0 cell line. e, Heatmap of Trim28 enrichment at DMRs. ChIP-seq of Trim28 shows enrichment over DMRs for all replicates from WT, TKOL, and DKO0 ESCs. The signal is displayed as fragment pile up per million reads per replicate.
