Transposon-derived transcription factor binding sites and promoter activities in breast cancer

Jiang J and Upton KR

The University of Queensland, The School of Chemistry and Molecular Biosciences.

Transposons, a type of repetitive DNA, are pervasive in the human genome, occupying approximately 45% of the total genomic sequence. Since their initial discovery by Barbara McClintock, transposons were predominantly viewed as junk or selfish DNA. However, recent progress has revealed the extensive co-option of transposons for the transcriptional regulation of host genes. While generally inactivated in normal somatic tissues, transposons can become transcriptionally active in epithelial cancers and may even act as promoters or enhancers that subsequently activate oncogenes and contribute to tumorigenesis. Currently, the regulatory impact of transposons in breast cancer remains largely unknown. To address this gap in knowledge, we investigated the landscape of transposon-derived oncogenic transcription factor (TF) binding in breast cancer, predicted transposon-derived promoters, and validated these predictions. Our results demonstrated that transposons were an abundant source of TF binding sites in breast cancer, where ~38% of all binding sites of MYC, E2F1 and C/EBPβ were harboured by transposons. We identified 399 transposon subfamilies as significantly overrepresented in the oncogenic TF binding sites, suggesting a widespread role of these subfamilies in cancer transcriptional networks. TF-bound transposons were also associated with active histone modifications, further supporting the regulatory role of transposons in breast cancer. Finally, we validated the promoter activity of individual transposons in triple negative breast cancer cell lines. Luciferase assay results revealed that the promoter activities of SYT1, UCA1, AK4 and PSAT1 oncogenes were significantly reduced, and in some cases, almost completely abolished following transposon deletion. Transposons with strong promoter activity were also found to be epigenetically deregulated in breast cancer, characterised by hypomethylation and/or increased DNAse sensitivity. Our results provide an insight into the contribution of transposons to breast cancer transcriptional regulation, and will facilitate the development of novel diagnostic and prognostic biomarkers for breast cancer.