Fig. 1

Methylation and expression profiles of CRISPR-Cas9 TET2-knockout cells. a Sanger sequencing chromatograms depict deletion sites observed in CR1 (green bar; heterozygous knockout) or CR2 (blue bar; functional homozygous knockout) which occur within the CRISPR guide RNA target site (orange bar). Mutant sequences for each knockout are shown, compared to the parental TET2 sequence above. b Western blot shows complete loss of both TET2 isoforms in CR1 and CR2 knockouts as compared to parental RWPE-1 cells (top). Ku80 loading control is shown on the bottom. c Methylation levels are globally increased in TET2-knockout cells, with more differentially methylated regions (DMRs) in the promoter, gene body, and overall in both knockouts as compared to RWPE-1 (DiffBind, p < 0.05, n = 2). CR2 exhibits higher methylation levels as compared to CR1.The graph depicts the number of DMRs exhibiting increased methylation as compared to RWPE-1 (for CR1 and CR2) or as compared to either knockout (for RWPE-1). d Gene expression profiles show comparable levels of upregulation and downregulation in both knockouts, with 17.3% and 4.5% more genes showing significant downregulation than upregulation (1.5-fold change, p < 0.05). e Visual depiction of gene selection to identify genes exhibiting both significant methylation in the promoter region and significant loss of expression in either knockout (left, CR1; right, CR2) as compared to the total number of methylated genes