Extended Data Fig. 8: CRISPR screens identify factors required for methylation maintenance in mESCs.

a) Rank plot for screens in serum conditions. Dashed horizontal line indicates the p-value threshold of 0.05. P-values were obtained using MAGeCK RRA (robust rank aggregation). Red dots indicate known heterochromatin factors associated with ICR regulation, blue dots indicate genes found in multiple screens, and green dots indicate the positive controls. b) Overview of CRISPR hits for the Airn and Kcnq1ot1 reporter cell lines grown in 2i conditions. Dashed horizontal line indicates the p-value threshold of 0.05 obtained using MAGeCK RRA (robust rank aggregation). c) Rank plot for screens in 2i conditions. Dashed horizontal line indicates the p-value threshold of 0.05 obtained using MAGeCK RRA (robust rank aggregation). d) Overview of CRISPR hits using the EpiTF library in the serum-grown Airn reporter cell line. Dashed horizontal line indicates the p-value threshold of 0.05 obtained using MAGeCK RRA (robust rank aggregation). e) Rank plot for the screen using the Airn pEF1a reporter in serum using the EpiTF library. Dashed horizontal line indicates the p-value threshold of 0.05 obtained using MAGeCK RRA (robust rank aggregation). f) Validation of potential candidates using single transfections of guide RNAs against the indicated gene. GFP expression was measured 12 days after transfection. Transfections were performed in technical replicates. Potential candidates were targeted with one independent guide and one guide from the ChromMM library. Data is showing % of positive cells in pools after CRISPR targeting. g) Network representation for all potential candidates using the STRING database. Pink edge indicates experimentally determined interactions; cyan edge indicates known interactions from curated databases. Green, red, and blue edges indicate predicted interactions based on gene neighbourhood, gene fusion, and gene co-occurrence, respectively. Yellow and black edges are predicted interactions based on textmining and co-expression, respectively.