LINE-1 Locus Transcription Nucleates Oncogenic Chromatin Architecture

Retrotransposons are genomic parasites frequently reactivated in cancers, in which their mobility can cause genetic alterations. However, it remains unclear whether their gene products contribute to cancer beyond mutagenesis. In this study, we uncover a chromatin-associated function of RNAs from long interspersed element-1 (LINE-1), the only autonomous retrotransposon in the human genome. Subcellular-resolved transcriptomics revealed that LINE-1 RNAs are primarily nascent transcripts produced by full-length, cell type-specific genomic copies of evolutionarily young subfamilies. Using a long-read chromosome conformation assay, we identified a class of highly interactive LINE-1 loci required for gene expression across cancer subtypes, revealing an unexpected regulatory role for LINE-1 locus transcription in oncogenic gene control. LINE-1 RNA depletion disrupted LINE-1-centric chromatin interactions and downregulated associated genes, whereas genomic insertion of an inducible LINE-1 generated de novo chromatin interactions in a transcription-dependent manner. Therefore, beyond their mutagenic potential, retrotransposons also regulate cancer gene expression by nucleating chromatin architecture through their transcriptional activity. SIGNIFICANCE: We developed a long-read chromatin conformation assay capable of resolving repetitive DNA, enabling the identification of highly interactive LINE-1 retrotransposon loci that nucleate chromatin architecture in cancer cells. This activity is driven by chromatin-associated LINE-1 transcripts, offering a biological rationale for the frequent reactivation of LINE-1 transcription in cancer.