Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response

PLoS One. 2018 Dec 11;13(12):e0208526. doi: 10.1371/journal.pone.0208526. eCollection 2018.

Abstract

Control of gene expression depends on genetics and environmental factors. The T-cell intracellular antigens T-cell intracellular antigen 1 (TIA1), TIA1-like/related protein (TIAL1/TIAR) and human antigen R (HuR/ELAVL1) are RNA-binding proteins that play crucial roles in regulating gene expression in both situations. This study used massive sequencing analysis to uncover molecular and functional mechanisms resulting from the short-time expression of the b isoforms of TIA1 and TIAR, and of HuR in HEK293 cells. Our gene profiling analysis identified several hundred differentially expressed genes (DEGs) and tens of alternative splicing events associated with TIA1b, TIARb and HuR overexpression. Gene ontology analysis revealed that the controlled expression of these proteins strongly influences the patterns of DEGs and RNA variants preferentially associated with development, reproduction, cell cycle, metabolism, autophagy and apoptosis. Mechanistically, TIA1b and TIARb isoforms display both common and differential effects on the regulation of gene expression, involving systematic perturbations of cell biosynthetic machineries (splicing and translation). The transcriptome outputs were validated using functional assays of the targeted cellular processes as well as expression analysis for selected genes. Collectively, our observations suggest that early TIA1b and TIARb expression operates to connect the regulatory crossroads to protective proteostasis responses associated with a survival quiescence phenotype.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Cell Proliferation
  • ELAV-Like Protein 1 / genetics
  • ELAV-Like Protein 1 / metabolism*
  • G1 Phase Cell Cycle Checkpoints
  • Gene Expression Profiling
  • Gene Ontology
  • HEK293 Cells
  • Humans
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • Proteostasis
  • RNA / genetics
  • RNA / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • T-Cell Intracellular Antigen-1 / genetics
  • T-Cell Intracellular Antigen-1 / metabolism*
  • Transcriptome*

Substances

  • ELAV-Like Protein 1
  • ELAVL1 protein, human
  • Protein Isoforms
  • RNA-Binding Proteins
  • T-Cell Intracellular Antigen-1
  • TIA1 protein, human
  • TIAL1 protein, human
  • RNA

Grants and funding

This work was supported by a grant from the Spanish Ministry of Economic Affairs and Competitiveness to JMI (BFU2014-57735R). The CBMSO receives institutional funding from Fundación Ramón Areces and Banco Santander. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.