4EHP-independent repression of endogenous mRNAs by the RNA-binding protein GIGYF2.

Abstract:

:Initially identified as a factor involved in tyrosine kinase receptor signaling, Grb10-interacting GYF protein 2 (GIGYF2) has later been shown to interact with the 5' cap-binding protein 4EHP as part of a translation repression complex, and to mediate post-transcriptional repression of tethered reporter mRNAs. A current model proposes that GIGYF2 is indirectly recruited to mRNAs by specific RNA-binding proteins (RBPs) leading to translation repression through its association with 4EHP. Accordingly, we recently observed that GIGYF2 also interacts with the miRNA-induced silencing complex and probably modulates its translation repression activity. Here we have further investigated how GIGYF2 represses mRNA function. In a tethering reporter assay, we identify three independent domains of GIGYF2 with repressive activity. In this assay, GIGYF2-mediated repression is independent of 4EHP but largely dependent on the CCR4/NOT complex that GIGYF2 recruits through multiple interfaces. Importantly, we show that GIGYF2 is an RBP and identify for the first time endogenous mRNA targets that recapitulate 4EHP-independent repression. Altogether, we propose that GIGYF2 has two distinct mechanisms of repression: one depends on 4EHP binding and mainly affects translation; the other is 4EHP-independent and involves the CCR4/NOT complex and its deadenylation activity.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Amaya Ramirez CC,Hubbe P,Mandel N,Béthune J

doi

10.1093/nar/gky198

subject

Has Abstract

pub_date

2018-06-20 00:00:00

pages

5792-5808

issue

11

eissn

0305-1048

issn

1362-4962

pii

4937549

journal_volume

46

pub_type

杂志文章
  • Function of the C-terminus of phi29 DNA polymerase in DNA and terminal protein binding.

    abstract::The thumb subdomain, located in various family B DNA polymerases in the C-terminal region, has been shown in their crystal structures to move upon binding of DNA, changing its conformation to nearly completely wrap around the DNA. It has therefore been involved in DNA binding. In agreement with this, partial proteolys...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh184

    authors: Truniger V,Lázaro JM,Salas M

    更新日期:2004-01-16 00:00:00

  • Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003.

    abstract::The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical entities in oncology, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in gen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg126

    authors: Huret JL,Dessen P,Bernheim A

    更新日期:2003-01-01 00:00:00

  • Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.

    abstract::A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexibl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku338

    authors: Dršata T,Špačková N,Jurečka P,Zgarbová M,Šponer J,Lankaš F

    更新日期:2014-06-01 00:00:00

  • PPT-DB: the protein property prediction and testing database.

    abstract::The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. orde...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm800

    authors: Wishart DS,Arndt D,Berjanskii M,Guo AC,Shi Y,Shrivastava S,Zhou J,Zhou Y,Lin G

    更新日期:2008-01-01 00:00:00

  • Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme.

    abstract::Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric recognition sites oriented head-to-head to elicit double-strand break 25-27 bp downstream of one of the two sites. The proposed DNA cleavage mechanism involves ATP-dependent DNA translocation. The sequence context of the recogni...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh899

    authors: Raghavendra NK,Rao DN

    更新日期:2004-10-22 00:00:00

  • RetrOryza: a database of the rice LTR-retrotransposons.

    abstract::Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl780

    authors: Chaparro C,Guyot R,Zuccolo A,Piégu B,Panaud O

    更新日期:2007-01-01 00:00:00

  • Improved nucleotide selectivity and termination of 3'-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates.

    abstract::We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1293

    authors: Litosh VA,Wu W,Stupi BP,Wang J,Morris SE,Hersh MN,Metzker ML

    更新日期:2011-03-01 00:00:00

  • A directed evolution design of a GCG-specific DNA hemimethylase.

    abstract::DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific modification of DNA and are becoming increasingly important tools for biotechnology. Here we describe a structure-guided rational protein design combined with random mutagenesis and selection to change the specificity of the H...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp772

    authors: Gerasimaite R,Vilkaitis G,Klimasauskas S

    更新日期:2009-11-01 00:00:00

  • Interaction of dimeric intercalating dyes with single-stranded DNA.

    abstract::The unsymmetrical cyanine dye thiazole orange homodimer (TOTO) binds to single-stranded DNA (ssDNA, M13mp18 ssDNA) to form a fluorescent complex that is stable under the standard conditions of electrophoresis. The stability of this complex is indistinguishable from that of the corresponding complex of TOTO with double...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.7.1215

    authors: Rye HS,Glazer AN

    更新日期:1995-04-11 00:00:00

  • Effects of heterologous downstream sequences on the activity of the HIV-1 promoter and its response to Tat.

    abstract::In HIV-1 infection, Tat acts at least in part to control transcriptional elongation by overcoming premature transcriptional termination. In some other genes this process is governed by DNA elements called attenuators in concert with cellular transcription factors. To understand the action of Tat more fully and explore...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.24.5017

    authors: Greenberg ME,Mathews MB

    更新日期:1997-12-15 00:00:00

  • Efficient reamplification of differential display products by transient ligation and thermal asymmetric PCR.

    abstract::A new method for specific reamplification of DDRT-PCR products is presented. After transient ligation of the primary DDRT-PCR fragments into a T-vector, the cDNAs of interest were reamplified by hemi-nested PCR and thermally asymmetric cycles. In contrast to the originally described protocol, this method of reamplific...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.4.1130

    authors: Bonnet S,Prévot G,Bourgouin C

    更新日期:1998-02-15 00:00:00

  • Loosened nucleosome linker folding in transcriptionally active chromatin of chicken embryo erythrocyte nuclei.

    abstract::We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP elect...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.24.7397

    authors: Grigoryev SA,Spirin KS,Krasheninnikov IA

    更新日期:1990-12-25 00:00:00

  • Specifically alkylated DNA fragments. Synthesis and physical characterization of d[CGC(O6Me)GCG] and d[CGT(O6Me)GCG].

    abstract::Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.10.3393

    authors: Kuzmich S,Marky LA,Jones RA

    更新日期:1983-05-25 00:00:00

  • Decreased expression of topoisomerase IIbeta in poly(ADP-ribose) polymerase-deficient cells.

    abstract::Recent studies with poly(ADP-ribose) polymerase (PARP)-deficient mice have highlighted the role of this enzyme in genomic stability and response to various genomic insults. In the absence of DNA damaging treatment, we report here that a PARP-deficient cell line (PARP-/-) established from knockout mice displays a decre...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.22.5134

    authors: Canitrot Y,de Murcia G,Salles B

    更新日期:1998-11-15 00:00:00

  • Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

    abstract::The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.1.55

    authors: Karp PD,Riley M,Paley SM,Pellegrini-Toole A,Krummenacker M

    更新日期:1999-01-01 00:00:00

  • Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy.

    abstract::Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the inciden...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnj034

    authors: Cattaruzza F,Cricenti A,Flamini A,Girasole M,Longo G,Prosperi T,Andreano G,Cellai L,Chirivino E

    更新日期:2006-02-28 00:00:00

  • Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.

    abstract::Genome-wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA-pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm1060

    authors: Macgregor S,Zhao ZZ,Henders A,Nicholas MG,Montgomery GW,Visscher PM

    更新日期:2008-04-01 00:00:00

  • Intracellular RNA cleavage by the hairpin ribozyme.

    abstract::Studies involving ribozyme-directed inactivation of targeted RNA molecules have met with mixed success, making clear the importance of methods to measure and optimize ribozyme activity within cells. The interpretation of biochemical assays for determining ribozyme activity in the cellular environment have been complic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.15.3494

    authors: Seyhan AA,Amaral J,Burke JM

    更新日期:1998-08-01 00:00:00

  • ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

    abstract::ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy datab...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1108

    authors: Brozovic M,Dantec C,Dardaillon J,Dauga D,Faure E,Gineste M,Louis A,Naville M,Nitta KR,Piette J,Reeves W,Scornavacca C,Simion P,Vincentelli R,Bellec M,Aicha SB,Fagotto M,Guéroult-Bellone M,Haeussler M,Jacox E,Lowe

    更新日期:2018-01-04 00:00:00

  • RORα switches transcriptional mode of ERRγ that results in transcriptional repression of CYP2E1 under ethanol-exposure.

    abstract::Increased cytochrome P450 2E1 (CYP2E1) expression is the main cause of oxidative stress, which exacerbates alcoholic liver diseases (ALDs). Estrogen-related receptor gamma (ERRγ) induces CYP2E1 expression and contributes to enhancing alcohol-induced liver injury. Retinoic acid-related orphan receptor alpha (RORα) has ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1034

    authors: Han YH,Kim DK,Na TY,Ka NL,Choi HS,Lee MO

    更新日期:2016-02-18 00:00:00

  • A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing.

    abstract::Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq667

    authors: Cantacessi C,Jex AR,Hall RS,Young ND,Campbell BE,Joachim A,Nolan MJ,Abubucker S,Sternberg PW,Ranganathan S,Mitreva M,Gasser RB

    更新日期:2010-09-01 00:00:00

  • The complete nucleotide sequence of the RNA coding for the primary translation product of foot and mouth disease virus.

    abstract::The complete nucleotide sequence of the coding region of foot and mouth disease virus RNA (strain A1061) is presented. The sequence extends from the primary initiation site, approximately 1200 nucleotide from the 5' end of the genome, in an open translational reading frame of 6,999 nucleotides to a termination codon 9...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.5.2461

    authors: Carroll AR,Rowlands DJ,Clarke BE

    更新日期:1984-03-12 00:00:00

  • The COG database: new developments in phylogenetic classification of proteins from complete genomes.

    abstract::The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.1.22

    authors: Tatusov RL,Natale DA,Garkavtsev IV,Tatusova TA,Shankavaram UT,Rao BS,Kiryutin B,Galperin MY,Fedorova ND,Koonin EV

    更新日期:2001-01-01 00:00:00

  • 2'-O-methyl, 2'-O-ethyl oligoribonucleotides and phosphorothioate oligodeoxyribonucleotides as inhibitors of the in vitro U7 snRNP-dependent mRNA processing event.

    abstract::We describe the synthesis of 2'-O-methyl, 2'-O-ethyl oligoribonucleotides and phosphorothioate oligodeoxyribonucleotides and demonstrate their utility as inhibitors of the in vitro U7 snRNP-dependent mRNA processing event. These 2'-O-modified compounds were designed to possess the binding affinity of an RNA molecule t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.10.2629

    authors: Cotten M,Oberhauser B,Brunar H,Holzner A,Issakides G,Noe CR,Schaffner G,Wagner E,Birnstiel ML

    更新日期:1991-05-25 00:00:00

  • Base excision repair processing of abasic site/single-strand break lesions within clustered damage sites associated with XRCC1 deficiency.

    abstract::Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm947

    authors: Mourgues S,Lomax ME,O'Neill P

    更新日期:2007-01-01 00:00:00

  • A circular trans-acting hepatitis delta virus ribozyme.

    abstract::A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of the 5' and 3' splice sites, flanking the single HDV-like ribozy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.18.4253

    authors: Puttaraju M,Perrotta AT,Been MD

    更新日期:1993-09-11 00:00:00

  • BYKdb: the Bacterial protein tYrosine Kinase database.

    abstract::Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure reso...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr915

    authors: Jadeau F,Grangeasse C,Shi L,Mijakovic I,Deléage G,Combet C

    更新日期:2012-01-01 00:00:00

  • Specificities of human, rat and E. coli O6-methylguanine-DNA methyltransferases towards the repair of O6-methyl and O6-ethylguanine in DNA.

    abstract::The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.9.1613

    authors: Liem LK,Lim A,Li BF

    更新日期:1994-05-11 00:00:00

  • Expanding the structural and functional diversity of RNA: analog uridine triphosphates as candidates for in vitro selection of nucleic acids.

    abstract::Two analog uridine triphosphates tethering additional functionality, one a primary amino group and the second a mercapto group, were prepared and tested for their compatibility with in vitro RNA selection procedures. 5-(3-Aminopropyl)uridine triphosphate (UNH(2)) as a uridine substitute was a more effective substrate ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.17.3316

    authors: Vaish NK,Fraley AW,Szostak JW,McLaughlin LW

    更新日期:2000-09-01 00:00:00

  • Functional characterization of C. elegans Y-box-binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes.

    abstract::The cold shock domain is one of the most highly conserved motifs between bacteria and higher eukaryotes. Y-box-binding proteins represent a subfamily of cold shock domain proteins with pleiotropic functions, ranging from transcription in the nucleus to translation in the cytoplasm. These proteins have been investigate...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1077

    authors: Arnold A,Rahman MM,Lee MC,Muehlhaeusser S,Katic I,Gaidatzis D,Hess D,Scheckel C,Wright JE,Stetak A,Boag PR,Ciosk R

    更新日期:2014-12-01 00:00:00