Supplementary Figures S1-S17 from LINE-1 Locus Transcription Nucleates Oncogenic Chromatin Architecture

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Figure S1. Subcellular localization of LINE-1 RNAs in cancer cells. Figure S2. Chromatin-associated LINE-1 RNAs are nascent transcripts associated in cis with their sites of transcription. Figure S3. Chromatin RNA-sequencing of human cancer cells and primary tumors to quantify locusspecific LINE-1 expression. Figure S4. Analysis of uniquely and multi-mapped reads by RNA-seq of LINE-1 expression. Figure S5. Identification of the expression cut-off for RNA-seq analysis of LINE-1 locus expression. Figure S6. Identification of cell type-specific LINE-1 locus expression in human cancer cell lines. Figure S7. Lineage-specific transcription factors and chromatin features regulate LINE-1 locus expression. Figure S8. LINE-1 Capture Pore-C for detecting LINE-1-centric chromatin interactions. Figure S9. Identification of LINE-1-centric chromatin interactions by L1CaP-C. Figure S10. Mappability analysis of L1CaP-C sequencing reads associated with chromatin interactions. Figure S11. LINE-1-centric chromatin interactions identified by L1CaP-C. Figure S12. Identification of highly interacting LINE-1 loci. Figure S13. L1CaP-C identifies pairwise and high-order chromatin interactions. Figure S14. Analysis of chromatin marks at HILL LINE-1 loci and super-enhancers (SEs). Figure S15. Correlation of HILL LINE-1 loci with clinical features in TCGA breast cancer samples. Figure S16. LINE-1 locus expression regulates oncogenic gene expression. Figure S17. LINE-1 depletion impairs cell proliferation and oncogenic gene expression.