Systematic Characterization of Stress-Induced RNA Granulation

Mol Cell. 2018 Apr 5;70(1):175-187.e8. doi: 10.1016/j.molcel.2018.02.025. Epub 2018 Mar 22.

Abstract

Upon stress, cytoplasmic mRNA is sequestered to insoluble ribonucleoprotein (RNP) granules, such as the stress granule (SG). Partially due to the belief that translationally suppressed mRNAs are recruited to SGs in bulk, stress-induced dynamic redistribution of mRNA has not been thoroughly characterized. Here, we report that endoplasmic reticulum (ER) stress targets only a small subset of translationally suppressed mRNAs into the insoluble RNP granule fraction (RG). This subset, characterized by extended length and adenylate-uridylate (AU)-rich motifs, is highly enriched with genes critical for cell survival and proliferation. This pattern of RG targeting was conserved for two other stress types, heat shock and arsenite toxicity, which induce distinct responses in the total cytoplasmic transcriptome. Nevertheless, stress-specific RG-targeting motifs, such as guanylate-cytidylate (GC)-rich motifs in heat shock, were also identified. Previously underappreciated, transcriptome profiling in the RG may contribute to understanding human diseases associated with RNP dysfunction, such as cancer and neurodegeneration.

Keywords: AU-rich elements; ER stress; RNA-seq; RNP granule; arsenite toxicity; heat shock; stress granule; transcriptome.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • AU Rich Elements
  • Animals
  • Arsenites / toxicity
  • Binding Sites
  • Cytoplasmic Granules / genetics
  • Cytoplasmic Granules / metabolism*
  • Endoplasmic Reticulum Stress* / drug effects
  • HCT116 Cells
  • HEK293 Cells
  • Heat-Shock Response*
  • Humans
  • Mice
  • NIH 3T3 Cells
  • Protein Binding
  • Proto-Oncogenes
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Ribonucleoproteins / genetics
  • Ribonucleoproteins / metabolism*
  • Solubility
  • Thapsigargin / toxicity
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcriptome* / drug effects

Substances

  • Arsenites
  • NORAD long non-coding RNA, human
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA-Binding Proteins
  • Ribonucleoproteins
  • Transcription Factors
  • pumilio protein, human
  • Thapsigargin
  • arsenite