Circular ANRIL isoforms switch from repressors to activators of p15/CDKN2B expression during RAF1 oncogene-induced senescence

RNA Biol. 2021 Mar;18(3):404-420. doi: 10.1080/15476286.2020.1812910. Epub 2020 Sep 29.

Abstract

Long non-coding RNAs (ncRNAs) are major regulators of gene expression and cell fate. The INK4 locus encodes the tumour suppressor proteins p15INK4b, p16INK4a and p14ARF required for cell cycle arrest and whose expression increases during senescence. ANRIL is a ncRNA antisense to the p15 gene. In proliferative cells, ANRIL prevents senescence by repressing INK4 genes through the recruitment of Polycomb-group proteins. In models of replicative and RASval12 oncogene-induced senescence (OIS), the expression of ANRIL and Polycomb proteins decreases, thus allowing INK4 derepression. Here, we found in a model of RAF1 OIS that ANRIL expression rather increases, due in particular to an increased stability. This led us to search for circular ANRIL isoforms, as circular RNAs are rather stable species. We found that the expression of two circular ANRIL increases in several OIS models (RAF1, MEK1 and BRAF). In proliferative cells, they repress p15 expression, while in RAF1 OIS, they promote full induction of p15, p16 and p14ARF expression. Further analysis of one of these circular ANRIL shows that it interacts with Polycomb proteins and decreases EZH2 Polycomb protein localization and H3K27me3 at the p15 and p16 promoters, respectively. We propose that changes in the ratio between Polycomb proteins and circular ANRIL isoforms allow these isoforms to switch from repressors of p15 gene to activators of all INK4 genes in RAF1 OIS. Our data reveal that regulation of ANRIL expression depends on the senescence inducer and underline the importance of circular ANRIL in the regulation of INK4 gene expression and senescence.

Keywords: INK4 locus; Non-coding RNAs; Polycomb proteins; circular RNAs; gene expression regulation; oncogene-induced senescence.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Cell Proliferation
  • Cellular Senescence / genetics*
  • Cyclin-Dependent Kinase Inhibitor p15 / genetics*
  • Gene Expression Regulation
  • Humans
  • Oncogenes
  • Proto-Oncogene Proteins c-raf / genetics*
  • RNA Isoforms
  • RNA Stability
  • RNA, Circular / genetics*
  • Tumor Necrosis Factor Ligand Superfamily Member 13 / genetics*
  • Tumor Necrosis Factor Ligand Superfamily Member 13 / metabolism

Substances

  • CDKN2B protein, human
  • Cyclin-Dependent Kinase Inhibitor p15
  • RNA Isoforms
  • RNA, Circular
  • Tumor Necrosis Factor Ligand Superfamily Member 13
  • Proto-Oncogene Proteins c-raf
  • Raf1 protein, human

Grant support

This work was supported by the Fondation ARC pour la Recherche sur le Cancer [PGA120150202320]; Fondation de France [185742_ 00087515]; Institut National du Cancer [DA N°2012-123]; Fondation Toulouse Cancer Santé [DRUGSPEED 2018-2]; Ligue Nationale Contre le Cancer [EL-190350].