Transposable elements drive widespread expression of oncogenes in human cancers

Nat Genet. 2019 Apr;51(4):611-617. doi: 10.1038/s41588-019-0373-3. Epub 2019 Mar 29.

Abstract

Transposable elements (TEs) are an abundant and rich genetic resource of regulatory sequences1-3. Cryptic regulatory elements within TEs can be epigenetically reactivated in cancer to influence oncogenesis in a process termed onco-exaptation4. However, the prevalence and impact of TE onco-exaptation events across cancer types are poorly characterized. Here, we analyzed 7,769 tumors and 625 normal datasets from 15 cancer types, identifying 129 TE cryptic promoter-activation events involving 106 oncogenes across 3,864 tumors. Furthermore, we interrogated the AluJb-LIN28B candidate: the genetic deletion of the TE eliminated oncogene expression, while dynamic DNA methylation modulated promoter activity, illustrating the necessity and sufficiency of a TE for oncogene activation. Collectively, our results characterize the global profile of TE onco-exaptation and highlight this prevalent phenomenon as an important mechanism for promiscuous oncogene activation and ultimately tumorigenesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Cell Line, Tumor
  • DNA Methylation / genetics
  • DNA Transposable Elements / genetics*
  • Evolution, Molecular
  • HEK293 Cells
  • Humans
  • K562 Cells
  • Neoplasms / genetics*
  • Oncogenes / genetics*
  • Promoter Regions, Genetic / genetics
  • Regulatory Sequences, Nucleic Acid / genetics

Substances

  • DNA Transposable Elements