Abstract

Aberrant expression of cancer genes and non-canonical RNA species is a hallmark of cancer. However, the mechanisms driving such atypical gene expression programs are incompletely understood. Here, our transcriptional profiling of a cohort of 50 primary clear cell renal cell carcinoma (ccRCC) samples from The Cancer Genome Atlas (TCGA) reveals that transcription read-through beyond the termination site is a source of transcriptome diversity in cancer cells. Amongst the genes most frequently mutated in ccRCC, we identified SETD2 inactivation as a potent enhancer of transcription read-through. We further show that invasion of neighbouring genes and generation of RNA chimeras are functional outcomes of transcription read-through. We identified the BCL2 oncogene as one of such invaded genes and detected a novel chimera, the CTSC-RAB38, in 20% of ccRCC samples. Collectively, our data highlight a novel link between transcription read-through and aberrant expression of oncogenes and chimeric transcripts that is prevalent in cancer.

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Author details

  1. Ana Rita Grosso

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  2. Ana Paula Leite

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  3. Sílvia Carvalho

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  4. Mafalda Ramos Matos

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  5. Filipa Batalha Martins

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  6. Alexandra Coitos Vítor

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  7. Joana MP Desterro

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  8. Maria Carmo-Fonseca

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  9. Sérgio Fernandes de Almeida

    Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
    For correspondence
    sergioalmeida@fm.ul.pt
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2015, Grosso et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Ana Rita Grosso
  2. Ana Paula Leite
  3. Sílvia Carvalho
  4. Mafalda Ramos Matos
  5. Filipa Batalha Martins
  6. Alexandra Coitos Vítor
  7. Joana MP Desterro
  8. Maria Carmo-Fonseca
  9. Sérgio Fernandes de Almeida
(2015)
Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma
eLife 4:e09214.
https://doi.org/10.7554/eLife.09214

Share this article

https://doi.org/10.7554/eLife.09214

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