Translational control of ERK signaling through miRNA/4EHP-directed silencing

MicroRNAs (miRNAs) exert a broad influence over gene expression by directing effector activities that impinge on translation and stability of mRNAs. We recently discovered that the cap-binding protein 4EHP is a key component of the mammalian miRNA-Induced Silencing Complex (miRISC), which mediates gene silencing. However, little is known about the mRNA repertoire that is controlled by the 4EHP/miRNA mechanism or its biological importance. Here, using ribosome profiling, we identify a subset of mRNAs that are translationally controlled by 4EHP. We show that the Dusp6 mRNA, which encodes an ERK1/2 phosphatase, is translationally repressed by 4EHP and a specific miRNA, miR-145. This promotes ERK1/2 phosphorylation, resulting in augmented cell growth and reduced apoptosis. Our findings thus empirically define the integral role of translational repression in miRNA-induced gene silencing and reveal a critical function for this process in the control of the ERK signaling cascade in mammalian cells.

[1]  B. Cohen,et al.  PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs , 2018, Nature Communications.

[2]  Kyle A. Cottrell,et al.  Translation efficiency is a determinant of the magnitude of miRNA-mediated repression , 2017, Scientific Reports.

[3]  P. Pfluger,et al.  Dual specificity phosphatase 6 deficiency is associated with impaired systemic glucose tolerance and reversible weight retardation in mice , 2017, PloS one.

[4]  G. Gao,et al.  MicroRNAs recruit eIF4E2 to repress translation of target mRNAs , 2017, Protein & Cell.

[5]  T. Tuschl,et al.  The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs , 2017, Nature Communications.

[6]  E. Valkov,et al.  GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression , 2017, Genes & development.

[7]  Christos G. Gkogkas,et al.  Cap-binding protein 4EHP effects translation silencing by microRNAs , 2017, Proceedings of the National Academy of Sciences.

[8]  Katherine A. Gallagher,et al.  Enhancement of macrophage inflammatory responses by CCL2 is correlated with increased miR-9 expression and downregulation of the ERK1/2 phosphatase Dusp6. , 2017, Cellular immunology.

[9]  Chao Yang,et al.  Differential Sensitivity of Target Genes to Translational Repression by miR-17~92 , 2017, PLoS genetics.

[10]  L. Harries,et al.  The DDX6–4E-T interaction mediates translational repression and P-body assembly , 2016, Nucleic acids research.

[11]  W. Filipowicz,et al.  Structure of a Human 4E-T/DDX6/CNOT1 Complex Reveals the Different Interplay of DDX6-Binding Proteins with the CCR4-NOT Complex. , 2015, Cell reports.

[12]  K. Coombes,et al.  Erk Negative Feedback Control Enables Pre-B Cell Transformation and Represents a Therapeutic Target in Acute Lymphoblastic Leukemia. , 2015, Cancer cell.

[13]  D. Bartel,et al.  Predicting effective microRNA target sites in mammalian mRNAs , 2015, eLife.

[14]  E. Izaurralde,et al.  Towards a molecular understanding of microRNA-mediated gene silencing , 2015, Nature Reviews Genetics.

[15]  Hongming Song,et al.  MicroRNA-145 inhibits human papillary cancer TPC1 cell proliferation by targeting DUSP6. , 2015, International journal of clinical and experimental medicine.

[16]  S. Shin,et al.  Constitutively active Ras negatively regulates Erk MAP kinase through induction of MAP kinase phosphatase 3 (MKP3) in NIH3T3 cells , 2014, BMB reports.

[17]  P. Poulikakos,et al.  Targeting RAS–ERK signalling in cancer: promises and challenges , 2014, Nature Reviews Drug Discovery.

[18]  Steven J. M. Jones,et al.  Integrated Genomic Characterization of Papillary Thyroid Carcinoma , 2014, Cell.

[19]  Daehyun Baek,et al.  mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. , 2014, Molecular cell.

[20]  Eva Benito,et al.  MicroRNA‐125b induces tau hyperphosphorylation and cognitive deficits in Alzheimer's disease , 2014, The EMBO journal.

[21]  Camille B Francisco,et al.  Microenvironment and Immunology Cancer Cells Exploit eIF 4 E 2-Directed Synthesis of Hypoxia Response Proteins to Drive Tumor Progression , 2014 .

[22]  S. Chandarlapaty,et al.  Rapid induction of apoptosis by PI3K inhibitors is dependent upon their transient inhibition of RAS-ERK signaling. , 2014, Cancer discovery.

[23]  N. Standart,et al.  Human 4E-T represses translation of bound mRNAs and enhances microRNA-mediated silencing , 2013, Nucleic acids research.

[24]  Richard A. Olshen,et al.  Assessing gene-level translational control from ribosome profiling , 2013, Bioinform..

[25]  Adam B. Olshen,et al.  The translational landscape of the mammalian cell cycle. , 2013, Molecular cell.

[26]  Feng Zhang,et al.  Genome engineering using CRISPR-Cas9 system. , 2015, Methods in molecular biology.

[27]  S. Keyse,et al.  Dual-specificity MAP kinase phosphatases (MKPs) , 2013, The FEBS journal.

[28]  F. Gebauer,et al.  Translational control by 3′-UTR-binding proteins , 2012, Briefings in functional genomics.

[29]  E. Krishnan,et al.  Decline in miR-181a expression with age impairs T cell receptor sensitivity by increasing DUSP6 activity , 2012, Nature Medicine.

[30]  W. Filipowicz,et al.  Kinetic analysis reveals successive steps leading to miRNA‐mediated silencing in mammalian cells , 2012, EMBO reports.

[31]  Anna M. McGeachy,et al.  The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments , 2012, Nature Protocols.

[32]  A. Gingras,et al.  A Novel 4EHP-GIGYF2 Translational Repressor Complex Is Essential for Mammalian Development , 2012, Molecular and Cellular Biology.

[33]  Carla Mattos,et al.  A comprehensive survey of Ras mutations in cancer. , 2012, Cancer research.

[34]  A. Giraldez,et al.  Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish , 2012, Science.

[35]  R. Green,et al.  miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay , 2012, Science.

[36]  D. Sabatini,et al.  A unifying model for mTORC1-mediated regulation of mRNA translation , 2012, Nature.

[37]  D. Sabatini,et al.  mTOR Signaling in Growth Control and Disease , 2012, Cell.

[38]  W. Filipowicz,et al.  HuR protein attenuates miRNA-mediated repression by promoting miRISC dissociation from the target RNA , 2012, Nucleic acids research.

[39]  V. Beneš,et al.  Kaposi's Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis , 2011, PLoS pathogens.

[40]  Nicholas T. Ingolia,et al.  Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.

[41]  J. Blenis,et al.  The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation. , 2011, Trends in biochemical sciences.

[42]  G. Pagès,et al.  Post‐transcriptional regulation of the DUSP6/MKP‐3 phosphatase by MEK/ERK signaling and hypoxia , 2011, Journal of cellular physiology.

[43]  R. Elkon,et al.  A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility , 2010, Nature Cell Biology.

[44]  Nicholas T. Ingolia,et al.  Mammalian microRNAs predominantly act to decrease target mRNA levels , 2010, Nature.

[45]  A. Borczuk,et al.  Dual specificity phosphatase 6 (DUSP6) is an ETS-regulated negative feedback mediator of oncogenic ERK signaling in lung cancer cells. , 2010, Carcinogenesis.

[46]  J. Chambard,et al.  ERK and cell death: Mechanisms of ERK‐induced cell death – apoptosis, autophagy and senescence , 2010, The FEBS journal.

[47]  J. Yates,et al.  Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. , 2009, Molecular cell.

[48]  Mark Gerstein,et al.  The relationship between the evolution of microRNA targets and the length of their UTRs , 2009, BMC Genomics.

[49]  P. Fischer.  Cap in hand: Targeting eIF4E , 2009, Cell cycle.

[50]  Ivet Bahar,et al.  Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages , 2009, Nature chemical biology.

[51]  Akhilesh Pandey,et al.  Identification of miR‐21 targets in breast cancer cells using a quantitative proteomic approach , 2009, Proteomics.

[52]  A. Hinnebusch,et al.  Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets , 2009, Cell.

[53]  Mihaela Zavolan,et al.  Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System , 2008, PloS one.

[54]  N. Rajewsky,et al.  Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.

[55]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[56]  G. Pagès,et al.  Post-translational regulation of the ERK phosphatase DUSP6/MKP3 by the mTOR pathway , 2008, Oncogene.

[57]  Christopher J. Staples,et al.  Negative-feedback regulation of FGF signalling by DUSP6/MKP-3 is driven by ERK1/2 and mediated by Ets factor binding to a conserved site within the DUSP6/MKP-3 gene promoter , 2008, The Biochemical journal.

[58]  Takayuki Murata,et al.  MicroRNA Inhibition of Translation Initiation in Vitro by Targeting the Cap-Binding Complex eIF4F , 2007, Science.

[59]  Tao Wang,et al.  Therapeutic suppression of translation initiation factor eIF4E expression reduces tumor growth without toxicity. , 2007, The Journal of clinical investigation.

[60]  S. Knapp,et al.  Structures of the human eIF4E homologous protein, h4EHP, in its m7GTP-bound and unliganded forms. , 2007, Journal of molecular biology.

[61]  Dang D. Long,et al.  Potent effect of target structure on microRNA function , 2007, Nature Structural &Molecular Biology.

[62]  Dong-er Zhang,et al.  ISG15 modification of the eIF4E cognate 4EHP enhances cap structure-binding activity of 4EHP. , 2007, Genes & development.

[63]  Daryl A. Scott,et al.  Dusp6 (Mkp3) is a negative feedback regulator of FGF-stimulated ERK signaling during mouse development , 2007, Development.

[64]  M. Wickens,et al.  LIP‐1 phosphatase controls the extent of germline proliferation in Caenorhabditis elegans , 2006, The EMBO journal.

[65]  W. Kolch.  Coordinating ERK/MAPK signalling through scaffolds and inhibitors , 2005, Nature Reviews Molecular Cell Biology.

[66]  N. Sonenberg,et al.  A New Paradigm for Translational Control: Inhibition via 5′-3′ mRNA Tethering by Bicoid and the eIF4E Cognate 4EHP , 2005, Cell.

[67]  F. Slack,et al.  RAS Is Regulated by the let-7 MicroRNA Family , 2005, Cell.

[68]  Amy R. Cameron,et al.  Characterization of mammalian eIF4E-family members. , 2004, European journal of biochemistry.

[69]  C. Tickle,et al.  Negative Feedback Regulation of FGF Signaling Levels by Pyst1/MKP3 in Chick Embryos , 2003, Current Biology.

[70]  J. C. Belmonte,et al.  MKP3 mediates the cellular response to FGF8 signalling in the vertebrate limb , 2003, Nature Cell Biology.

[71]  B. Henderson.  Post-Transcriptional Regulation , 2002 .

[72]  A. Gingras,et al.  Cloning and Characterization of 4EHP, a Novel Mammalian eIF4E-related Cap-binding Protein* , 1998, The Journal of Biological Chemistry.

[73]  M. Muda,et al.  Catalytic activation of the phosphatase MKP-3 by ERK2 mitogen-activated protein kinase. , 1998, Science.

[74]  G. Cooper,et al.  Ras links growth factor signaling to the cell cycle machinery via regulation of cyclin D1 and the Cdk inhibitor p27KIP1 , 1997, Molecular and cellular biology.

[75]  Tony Hunter,et al.  MNK1, a new MAP kinase‐activated protein kinase, isolated by a novel expression screening method for identifying protein kinase substrates , 1997, The EMBO journal.

[76]  Michael E. Greenberg,et al.  Opposing Effects of ERK and JNK-p38 MAP Kinases on Apoptosis , 1995, Science.

[77]  H. Kretzschmar,et al.  MicroRNA-125 b induces tau hyperphosphorylation and cognitive deficits in Alzheimer ’ s disease , 2014 .

[78]  Christos G. Gkogkas,et al.  The cap-binding protein 4 EHP effects translation silencing by microRNAs , 2022 .

[79]  Daryl A. Scott,et al.  Dusp 6 ( Mkp 3 ) is a negative feedback regulator of FGF-stimulated ERK signaling during mouse development , 2022 .