Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression

PLoS One. 2015 May 20;10(5):e0125745. doi: 10.1371/journal.pone.0125745. eCollection 2015.

Abstract

Growing evidence suggests a key role for RNA binding proteins (RBPs) in genome stability programs. Additionally, recent developments in RNA sequencing technologies, as well as mass-spectrometry techniques, have greatly expanded our knowledge on protein-RNA interactions. We here use full transcriptome sequencing and label-free LC/MS/MS to identify global changes in protein-RNA interactions in response to etoposide-induced genotoxic stress. We show that RBPs have distinct binding patterns in response to genotoxic stress and that inactivation of the RBP regulator module, p38/MK2, can affect the entire spectrum of protein-RNA interactions that take place in response to stress. In addition to validating the role of known RBPs like Srsf1, Srsf2, Elavl1 in the genotoxic stress response, we add a new collection of RBPs to the DNA damage response. We identify Khsrp as a highly regulated RBP in response to genotoxic stress and further validate its role as a driver of the G(1/)S transition through the suppression of Cdkn1a(P21) transcripts. Finally, we identify KHSRP as an indicator of overall survival, as well as disease free survival in glioblastoma multiforme.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cells, Cultured
  • Cyclin-Dependent Kinase Inhibitor p21 / genetics
  • DNA Damage / genetics
  • Disease-Free Survival
  • ELAV-Like Protein 1 / genetics
  • G1 Phase Cell Cycle Checkpoints / genetics*
  • Gene Expression Profiling / methods*
  • Glioblastoma / genetics
  • Humans
  • Intracellular Signaling Peptides and Proteins / genetics*
  • Mice
  • Nuclear Proteins / genetics
  • Protein-Serine-Threonine Kinases / genetics*
  • RNA / genetics*
  • RNA-Binding Proteins / genetics*
  • Ribonucleoproteins / genetics
  • Serine-Arginine Splicing Factors
  • Signal Transduction / genetics
  • Trans-Activators / genetics*
  • p38 Mitogen-Activated Protein Kinases / genetics*

Substances

  • Cyclin-Dependent Kinase Inhibitor p21
  • ELAV-Like Protein 1
  • Elavl1 protein, mouse
  • Intracellular Signaling Peptides and Proteins
  • KHSRP protein, human
  • Nuclear Proteins
  • RNA-Binding Proteins
  • Ribonucleoproteins
  • SRSF2 protein, mouse
  • Trans-Activators
  • Serine-Arginine Splicing Factors
  • RNA
  • MAP-kinase-activated kinase 2
  • Protein-Serine-Threonine Kinases
  • p38 Mitogen-Activated Protein Kinases

Grant support

This work was supported by the Volkswagenstiftung (Lichtenberg Program H.C.R.), the Deutsche Forschungsgemeinschaft (KFO-286, RE2246/2-1 to H.C.R.), the Helmholtz-Gemeinschaft (Preclinical Comprehensive Cancer Center to H.C.R.), Federal Ministry for Research and Education (BMBF, 01ZX1303A to H.C.R.), the Else Kröner-Fresenius Stiftung (EKFS-2014-A06 to H.C.R.), the Deutsche Krebshilfe (DKH-111112 to H.C.R.) and Deutsche Jose Carreras Stiftung (DJCLS-R12/26 to H.C.R.).