Figure 1. LncRNA CRISPR screen hits within copy number amplified regions or overlapping protein-coding genes.

K562 lncRNA screen scores, 1 Mb window median of protein-coding screen scores³, and relative copy number (a) across the genome and (b) on chromosome 22. LncRNA screen scores are more positive for confident hits and protein-coding screen scores are negative for stronger fitness defects. (c) Relationship between relative copy number and window median coding gene phenotype. For each gene, relative copy number was averaged across the gene locus where data were available. Ribosomal subunits included in the screen as positive controls are also plotted for comparison. (d) Boxplots of lncRNA screen scores for each cell line separated by genes located in amplified regions and overlapping coding exons. The minimum score across all three cell lines is also plotted to identify lncRNAs scoring in each cell line. Boxplots show 25^th, 50^th, and 75^th percentiles, with whiskers indicating 1.5× inter-quartile range and outliers individually plotted. Horizontal line represents a screen score of 2 used as the threshold for hits by Liu et al.¹