Fig. 3
From: Genome-wide tracking of dCas9-methyltransferase footprints
Global off-target CpG methylation after transient dCas9-cat3a transfection. a 293T human embryonic kidney and MCF7 human breast cancer cells were transfected with pdCas9-DNMT3A-EGFP (Addgene #71666) or pdCas9-DNMT3A-EGFP (ANV) (Addgene #71685) with an sgRNA targeting BACH2. Cells were collected 3 days post-transfection (p.t.) and RRBS was performed. b Top: loess-smoothed CpG methylation for 293T cells (WGBS) highlighting the location of the BACH2 target within a CpG island. Bottom: the on-target smoothed methylation levels (RRBS) for 293T cells transfected with dCas9-cat3a or dCas9-cat3a-ANV 3 days p.t. The bold line indicates the mean methylation level with standard deviation shown by shaded fill. The position and orientation of the Bach2 sgRNA is indicated with a red arrow. c same as in b but for MCF7 cells. d Smooth scatter plot displaying mean methylation over 200 bp tiles in dCas9-cat3a and dCas9-cat3a-ANV transfected 293T cells 3 days p.t. with the Bach2 sgRNA (total tiles: 219,949). Red dots indicate tiles with significant changes in methylation (adj. p-value < 0.05 (t-test) and difference >10%, significant tiles: 32,665). The BACH2 locus is significant and highlighted as a white dot. e Same as in d but for MCF7 cells (total tiles: 200,157; significant tiles: 10,881). f The proportion of significantly differentially methylated 200 bp tiles that are located within CpG islands (CGIs) for 293T and MCF7 cells. g Methylation levels for CGIs that have <10% methylation in WT cells shown for dCas9–cat3a–ANV and dCas9–cat3a transfected 293T/MCF7 cells
