Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates

Genes Dev. 2013 Jul 15;27(14):1624-32. doi: 10.1101/gad.215939.113. Epub 2013 Jul 3.

Abstract

When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Argonaute 2 (Ago2)/microRNA (miRNA) machinery has been shown to participate in stress-induced translational up-regulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by cross-linking immunoprecipitation (CLIP) followed by high-throughput sequencing (CLIP-seq). Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3' untranslated region (UTR) and coding sequence (CDS) sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2-binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA sequencing (RNA-seq). Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian miRNAs in mediating the translational component of the stress response.

Keywords: Argonaute; CLIP; microRNA; stress; translation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics
  • Amino Acid Motifs
  • Argonaute Proteins / genetics
  • Argonaute Proteins / metabolism*
  • Arsenites / pharmacology
  • Cell Line
  • Enzyme Inhibitors / pharmacology
  • Gene Expression Regulation*
  • HeLa Cells
  • Humans
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism*
  • Molecular Sequence Data
  • Protein Binding / drug effects
  • RNA, Messenger / metabolism*
  • Stress, Physiological / drug effects

Substances

  • 3' Untranslated Regions
  • AGO2 protein, human
  • Argonaute Proteins
  • Arsenites
  • Enzyme Inhibitors
  • MicroRNAs
  • RNA, Messenger
  • arsenite

Associated data

  • GENBANK/GSE44404