Fig. 3

Demethylated L1 elements act as alternative promotors and drive the expression of neuronal genes. a The expression of genes within 50 kb of upregulated L1s, FL-HERVs, and SVAs upon DNMT1-KO (n = 3 in both groups), p < 0.05, Wilcoxon rank sum test. The black dot shows the mean expression. b The expression of genes that lie within 50 kb of upregulated L1-HS, L1-PA2, L1-PA3. c Heatmaps of WGBS, RNA-seq, ChIP-seq of Pol II and H3K27ac in control and DNMT1-KO hNPCs of genes that lie within 50 kb of upregulated L1-HS, L1-PA2 and L1-PA3. d UCSC screenshots of two examples of L1-fusion transcripts. Blue boxes are indicating the reads that are initiated in the L1s. e A heatmap showing the relative expression of L1-exon fusion reads in three biological replicates of DNMT1-KO and control hNPCs. Only L1-exon fusion reads for genes in which the L1 overlap annotated TSS are included. f A heatmap showing the expression of L1-driven genes upon neuronal differentiation of hNPCs (n = 2 at all timepoints). Only genes that are significantly upregulated in DNMT1-KO hNPCs and have a hominoid-specific L1-TSS overlap as well as L1-exon fusion reads in the neuronal differentiation data are included. g A GO analysis of the L1-driven genes, using Panther BP ontologies, p < 0.05 (p = 0.05 is indicated with a dotted line). The top 10 terms are listed, for a full list see Supplementary Data 3