Extended Data Fig. 2: Intricate control of L1 expression in K562.

a, Bar plots showing the percentage of unique-mapped and multiple-mapped reads in indicated full-length L1PA subfamilies. b, Box plot showing the percentage of unique-mapped reads in individual full-length L1PAs (left), and the numbers of all elements and those that surpass the 5-read-count cutoff within each L1 subfamily (right). Center lines represent the median value, box limits represent the 25th and 75th percentiles and whiskers denote minima and maxima (1.5× the interquartile range). n = 2 biological replicates. c, Representative genome browser snapshots of the RNA-seq reads alignment over L1s. The color scale indicates the mapping quality score MAPQ for each read pair. MAPQ = −10 log₁₀(p), where p is the probability that true alignment belongs elsewhere. d, Heatmaps showing expression change of significantly changed L1PAs using unique mapping (top) or multiple mapping (bottom) in indicated mutant K562. n = 2 biological replicates per gene. P < 0.05, DESeq2 analysis. e, Mean splicing efficiency of the RNA-seq samples, calculated using SPLICE-q⁷⁹. f, Intronic read fraction of the RNA-seq samples, calculated using RNA-SeQC⁸⁰. Together with e, these results indicated the high quality of our RNA-seq library. g, Bubble plots showing expression change of L1, LTR and SINE subfamilies in indicated mutant K562. Multi-mapped reads were used to quantify transposons at the subfamily level. Colored circles represent the log₂ fold change, with areas proportional to P value (DESeq2 analysis). LTR, long terminal repeat; SINE, short interspersed nuclear element. n = 2 or 3 biological replicates per gene. h, Heatmap showing expression change at individual L1 locus in indicated mutant K562 (labeled and aligned same as in d). Hierarchical clustering was performed by ‘ward.D2’ method. RNA-seq reads were unique-mapped to individual L1 locus. Only significantly changed full-length L1s in at least one KO experiment were included (n = 222). P < 0.05, DESeq2 analysis. i,j, RNA-seq genome browser snapshots at six L1 loci from control and indicated mutant K562, illustrating that candidate L1 suppressors (i) and activators (j) selectively and cooperatively control L1 expression. The experiment was repeated once with similar results.