Extended Data Fig. 1: Genome-wide CRISPR–Cas9 screening for genes that control L1 expression in K562 cells.

a, Heatmap showing the relative expression of individual full-length L1s across three indicated human cell lines. Z-score transformed transcripts per million (TPM) values were used to represent L1 expression. b, L1 RNA quantification in K562 using the strand-specific polyA+ RNA-seq. Data are representative of two independent experiments. The center value is the mean. P, two-tailed t test. n.s., non-significant. c, Fluorescence-activated cell sorting results show that over 99% of the L1-GFP K562 cell clones express blue fluorescent protein (BFP)-Cas9 and L1-GFP. d, Chromosome maps showing the genomic distribution of 51 L1-GFP reporter insertions in the K562 screening cell line, measured by long-read sequencing. The individual genomic locations are listed in Supplementary Table 1. e, Normalized L1-GFP expression (left) and line plots showing GFP intensity (right) in control and mutant K562 as indicated. The center value is the mean. n = 2 biological replicates for MPP8, n = 3 biological replicates for SAFB and control. Knockout of known L1 suppressors (SAFB, MPP8) increased L1 expression. f, Correlation of the sgRNA counts of each sample in K562 genome-wide screens, relative to Fig. 1a. g, Enrichment values of the top 80 L1 suppressors (blue) and the top 80 activators (red) were calculated from two independent K562 genome-wide screens with 4 independent sgRNAs per gene. Diamond represents the mean value; whisker represents the fold range for sgRNAs. Previously characterized L1 regulators are marked with stars. h, Cytoscape for visualizing protein–protein interactions for L1 suppressors (blue) and L1 activators (red). i,j, Venn diagram showing the number of candidate L1 activators (i) and suppressors (j) identified in this screen against L1 expression (blue), and that identified from one previous screen against L1 retrotransposition¹⁶ (yellow) in K562. k,l, Gene ontology (biological process) enrichment analysis of the unique activators (k) and unique suppressors (l) identified in this screen against L1 expression, and that identified from one previous screen against L1 retrotransposition in K562 (ref. ¹⁶). P, one-tailed hypergeometric test.