3' UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk

Nat Genet. 2018 Jun;50(6):783-789. doi: 10.1038/s41588-018-0118-8. Epub 2018 May 21.

Abstract

Widespread mRNA 3' UTR shortening through alternative polyadenylation 1 promotes tumor growth in vivo 2 . A prevailing hypothesis is that it induces proto-oncogene expression in cis through escaping microRNA-mediated repression. Here we report a surprising enrichment of 3'UTR shortening among transcripts that are predicted to act as competing-endogenous RNAs (ceRNAs) for tumor-suppressor genes. Our model-based analysis of the trans effect of 3' UTR shortening (MAT3UTR) reveals a significant role in altering ceRNA expression. MAT3UTR predicts many trans-targets of 3' UTR shortening, including PTEN, a crucial tumor-suppressor gene 3 involved in ceRNA crosstalk 4 with nine 3'UTR-shortening genes, including EPS15 and NFIA. Knockdown of NUDT21, a master 3' UTR-shortening regulator 2 , represses tumor-suppressor genes such as PHF6 and LARP1 in trans in a miRNA-dependent manner. Together, the results of our analysis suggest a major role of 3' UTR shortening in repressing tumor-suppressor genes in trans by disrupting ceRNA crosstalk, rather than inducing proto-oncogenes in cis.

Publication types

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

MeSH terms

  • 3' Untranslated Regions*
  • Cell Line, Tumor
  • Gene Expression Regulation, Neoplastic
  • Genes, Tumor Suppressor*
  • HeLa Cells
  • Humans
  • MCF-7 Cells
  • MicroRNAs / genetics
  • Neoplasms / genetics*
  • Proto-Oncogene Mas
  • Proto-Oncogenes / genetics
  • RNA / genetics*
  • RNA, Messenger / genetics

Substances

  • 3' Untranslated Regions
  • MAS1 protein, human
  • MicroRNAs
  • Proto-Oncogene Mas
  • RNA, Messenger
  • RNA