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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

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An atlas of transposable element-derived alternative splicing in cancer

Evan A Clayton1, Lavanya Rishishwar2,3,4, Tzu-Chuan Huang2

  • 1Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|February 21, 2020
PubMed

Insights

Transposable elements (TEs) significantly contribute to alternative splicing in cancer, generating thousands of new splice variants in hundreds of genes. These TE-derived isoforms are linked to cancer development and novel fusion transcripts.

Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Transposable elements (TEs) constitute over half of the human genome.
  • TEs influence gene expression, including alternative splicing, which is implicated in cancer.

Purpose of the Study:

  • To broadly investigate the role of human TEs in generating alternatively spliced transcript isoforms in cancer.
  • To screen for TE-derived sequences at differentially used alternative splice sites in normal versus cancer tissues.

Main Methods:

  • Analysis of alternative splice variants from 614 matched normal-tumour tissue pairs across 13 cancer types.
  • Screening for TE sequences co-located with alternative splice sites.
  • Identification and characterization of TE-generated alternative splice events.

Main Results:

  • Discovery of 4820 TE-generated alternative splice events in 723 cancer-associated genes.
  • Short interspersed nuclear elements (Alu) and long interspersed nuclear elements (L1) were major contributors.
  • Overexpression of TE-derived isoforms in genes like MYH11, WHSC1, and CANT1 was observed across various cancers.

Conclusions:

  • Human TEs play a substantial role in generating alternative splicing in cancer.
  • TEs contribute to transcriptome diversity and potentially drive tumorigenesis through novel splice variants and fusion transcripts.
  • TE-mediated trans-splicing represents a novel mechanism for generating transcriptome diversity in cancer.
Keywords:
alternative splicingcancergene expressiongene regulationtransposable elementstumorigenesis

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