Proteins involved in the degradation of cytoplasmic mRNA in the major eukaryotic model systems

Organizing Principles of Mammalian Nonsense-Mediated mRNA Decay

(2013) Maximilian Wei-Lin Popp et al.   Annual Review of Genetics

RNA decay machines: Deadenylation by the Ccr4–Not and Pan2–Pan3 complexes

(2013) Elmar Wahle et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA decay via 3′ uridylation

(2013) Daniel D. Scott et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA decay machines: The exosome

(2013) Aleksander Chlebowski et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex

(2013) Felix Halbach et al.   CELL

Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation

(2013) Donghui Wu et al.   CELL RESEARCH

Exonuclease hDIS3L2 specifies an exosome-independent 3′-5′ degradation pathway of human cytoplasmic mRNA

(2013) Michal Lubas et al.   EMBO JOURNAL

The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway

(2013) Michal Malecki et al.   EMBO JOURNAL

Protein segregase meddles in remodeling of mRNA-protein complexes

(2013) C.-Y. A. Chen et al.   GENES & DEVELOPMENT

An unusual arrangement of two 14-3-3-like domains in the SMG5-SMG7 heterodimer is required for efficient nonsense-mediated mRNA decay

(2013) S. Jonas et al.   GENES & DEVELOPMENT

RNA deadenylation and decay in plants

(2013) Nazia Abbasi et al.   JOURNAL OF PLANT BIOLOGY

Pdc1 Functions in the Assembly of P Bodies in Schizosaccharomyces pombe

(2013) Chun-Yu Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

Argonaute and Triman Generate Dicer-Independent priRNAs and Mature siRNAs to Initiate Heterochromatin Formation

(2013) Mirela Marasovic et al.   MOLECULAR CELL

Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

(2013) Mai Sun et al.   MOLECULAR CELL

A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28–let-7 pathway

(2013) Hao-Ming Chang et al.   NATURE

Structure and RNA-binding properties of the Not1–Not2–Not5 module of the yeast Ccr4–Not complex

(2013) Varun Bhaskar et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA exosome complex central channel controls both exonuclease and endonuclease Dis3 activities in vivo and in vitro

(2013) Karolina Drążkowska et al.   NUCLEIC ACIDS RESEARCH

Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1

(2013) Clarivel Lasalde et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation of the N- and C-terminal UPF1 domains plays a critical role in plant nonsense-mediated mRNA decay

(2013) Farkas Kerényi et al.   PLANT JOURNAL

Arabidopsis AtRRP44A Is the Functional Homolog of Rrp44/Dis3, an Exosome Component, Is Essential for Viability and Is Required for RNA Processing and Degradation

(2013) Naoyoshi Kumakura et al.   PLoS One

Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs

(2013) D. Ustianenko et al.   RNA

Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways

(2013) S. Metze et al.   RNA

Structure of Histone mRNA Stem-Loop, Human Stem-Loop Binding Protein, and 3'hExo Ternary Complex

(2013) D. Tan et al.   SCIENCE

Architecture of the Lsm1-7-Pat1 Complex: A Conserved Assembly in Eukaryotic mRNA Turnover

(2013) Humayun Sharif et al.   Cell Reports

A genome-wide resource of cell cycle and cell shape genes of fission yeast

(2013) J. Hayles et al.   Open Biology

Alternative Splicing and Subfunctionalization Generates Functional Diversity in Fungal Proteomes

(2013) Alexandra N. Marshall et al.   PLoS Genetics

Deadenylation of cytoplasmic mRNA by the mammalian Ccr4–Not complex

(2012) Rachel Doidge et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A Translation-Like Cycle Is a Quality Control Checkpoint for Maturing 40S Ribosome Subunits

(2012) Bethany S. Strunk et al.   CELL

Mono-Uridylation of Pre-MicroRNA as a Key Step in the Biogenesis of Group II let-7 MicroRNAs

(2012) Inha Heo et al.   CELL

The Arabidopsis Nucleotidyl Transferase HESO1 Uridylates Unmethylated Small RNAs to Trigger Their Degradation

(2012) Yuanyuan Zhao et al.   CURRENT BIOLOGY

RNA Degradation in Saccharomyces cerevisae

(2012) Roy Parker   GENETICS

Dom34:Hbs1 Plays a General Role in Quality-Control Systems by Dissociation of a Stalled Ribosome at the 3′ End of Aberrant mRNA

(2012) Tatsuhisa Tsuboi et al.   MOLECULAR CELL

Erratum: Regulation of cytoplasmic mRNA decay

(2012) Daniel R. Schoenberg et al.   NATURE REVIEWS GENETICS

Surveillance pathways rescuing eukaryotic ribosomes lost in translation

(2012) Marc Graille et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Eri1 degrades the stem-loop of oligouridylated histone mRNAs to induce replication-dependent decay

(2012) Kai P Hoefig et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translation drives mRNA quality control

(2012) Christopher J Shoemaker et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5′ exonucleolytic degradation

(2012) Joerg E Braun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors is caused by autoimmune-like response

(2012) Nina Riehs-Kearnan et al.   NUCLEIC ACIDS RESEARCH

The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets

(2012) Eric Huntzinger et al.   NUCLEIC ACIDS RESEARCH

The late steps of plant nonsense-mediated mRNA decay

(2012) Zsuzsanna Mérai et al.   PLANT JOURNAL

Drosophila mutants show NMD pathway activity is reduced, but not eliminated, in the absence of Smg6

(2012) K. A. Frizzell et al.   RNA

mRNAs containing the histone 3' stem-loop are degraded primarily by decapping mediated by oligouridylation of the 3' end

(2012) W. Su et al.   RNA

Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes

(2011) Vera P Pisareva et al.   EMBO JOURNAL

The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex

(2011) Simon A Fromm et al.   EMBO JOURNAL

Not4 E3 Ligase Contributes to Proteasome Assembly and Functional Integrity in Part through Ecm29

(2011) O. O. Panasenko et al.   MOLECULAR AND CELLULAR BIOLOGY

The Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the human Ccr4–Not complex contribute to the prevention of cell death and senescence

(2011) Saloni Mittal et al.   MOLECULAR BIOLOGY OF THE CELL

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

PomBase: a comprehensive online resource for fission yeast

(2011) V. Wood et al.   NUCLEIC ACIDS RESEARCH

Interactions between Upf1 and the Decapping Factors Edc3 and Pat1 in Saccharomyces cerevisiae

(2011) Kylie D. Swisher et al.   PLoS One

Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast

(2011) C. J. Shoemaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs

(2011) D. Schaeffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories

(2011) L. A. Rymarquis et al.   RNA

The Pioneer Round of Translation: Features and Functions

(2010) Lynne E. Maquat et al.   CELL

Upf1 ATPase-Dependent mRNP Disassembly Is Required for Completion of Nonsense- Mediated mRNA Decay

(2010) Tobias M. Franks et al.   CELL

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Splicing-dependent NMD does not require the EJC in Schizosaccharomyces pombe

(2010) Jikai Wen et al.   EMBO JOURNAL

The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L

(2010) Rafal Tomecki et al.   EMBO JOURNAL

Hen1 is required for oocyte development and piRNA stability in zebrafish

(2010) Leonie M Kamminga et al.   EMBO JOURNAL

RNA channelling by the eukaryotic exosome

(2010) Hélène Malet et al.   EMBO REPORTS

Receptor for activated C kinase 1 stimulates nascent polypeptide-dependent translation arrest

(2010) Kazushige Kuroha et al.   EMBO REPORTS

HPat provides a link between deadenylation and decapping in metazoa

(2010) Gabrielle Haas et al.   JOURNAL OF CELL BIOLOGY

Identification and Analysis of the Interaction between Edc3 and Dcp2 in Saccharomyces cerevisiae

(2010) Y. Harigaya et al.   MOLECULAR AND CELLULAR BIOLOGY

Multiple mRNA Decapping Enzymes in Mammalian Cells

(2010) Man-Gen Song et al.   MOLECULAR CELL

Decapping Activators in Saccharomyces cerevisiae Act by Multiple Mechanisms

(2010) Tracy Nissan et al.   MOLECULAR CELL

Role of a ribosome-associated E3 ubiquitin ligase in protein quality control

(2010) Mario H. Bengtson et al.   NATURE

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

(2010) Dong-Uk Kim et al.   NATURE BIOTECHNOLOGY

Structure of the Dom34–Hbs1 complex and implications for no-go decay

(2010) Liming Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dissection of Dom34–Hbs1 reveals independent functions in two RNA quality control pathways

(2010) Antonia M G van den Elzen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Drosophila melanogaster Dis3 N-terminal domains are required for ribonuclease activities, nuclear localization and exosome interactions

(2010) Megan Mamolen et al.   NUCLEIC ACIDS RESEARCH

Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex

(2010) Kan Kobayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas

(2010) Fadia Ibrahim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lsm1-7-Pat1 complex:  A link between 3’ and 5’-ends in mRNA decay?

(2010) Sundaresan Tharun   RNA Biology

The exozyme model: A continuum of functionally distinct complexes

(2010) D. L. Kiss et al.   RNA

Translational competence of ribosomes released from a premature termination codon is modulated by NMD factors

(2010) S. Ghosh et al.   RNA

Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation

(2010) C. Temme et al.   RNA

The human cytoplasmic RNA terminal U-transferase ZCCHC11 targets histone mRNAs for degradation

(2010) M.-J. Schmidt et al.   RNA

Dom34:Hbs1 Promotes Subunit Dissociation and Peptidyl-tRNA Drop-Off to Initiate No-Go Decay

(2010) C. J. Shoemaker et al.   SCIENCE

Structural and functional insights into eukaryotic mRNA decapping

(2010) Sharon H. M. Ling et al.   Wiley Interdisciplinary Reviews-RNA

Regulation of mRNA decapping

(2010) You Li et al.   Wiley Interdisciplinary Reviews-RNA

Mechanisms of deadenylation-dependent decay

(2010) Chyi-Ying A. Chen et al.   Wiley Interdisciplinary Reviews-RNA

Human Ccr4–Not complexes contain variable deadenylase subunits

(2009) Nga-Chi Lau et al.   BIOCHEMICAL JOURNAL

CDE-1 Affects Chromosome Segregation through Uridylation of CSR-1-Bound siRNAs

(2009) Josien C. van Wolfswinkel et al.   CELL

The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation

(2009) Fabien Bonneau et al.   CELL

SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay

(2009) A. Yamashita et al.   GENES & DEVELOPMENT

Nascent Peptide-dependent Translation Arrest Leads to Not4p-mediated Protein Degradation by the Proteasome

(2009) Lyudmila N. Dimitrova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

mRNA Degradation Machinery in Plants

(2009) Yukako Chiba et al.   JOURNAL OF PLANT BIOLOGY

A Convergence of rRNA and mRNA Quality Control Pathways Revealed by Mechanistic Analysis of Nonfunctional rRNA Decay

(2009) Sarah E. Cole et al.   MOLECULAR CELL

Decapping is preceded by 3′ uridylation in a novel pathway of bulk mRNA turnover

(2009) Olivia S Rissland et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long 3′-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae

(2009) Bessie W. Kebaara et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Decapping 5 Is Required for mRNA Decapping, P-Body Formation, and Translational Repression during Postembryonic Development

(2009) J. Xu et al.   PLANT CELL

Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner

(2009) Tünde Nyikó et al.   PLANT MOLECULAR BIOLOGY

Arabidopsis Deadenylases AtCAF1a and AtCAF1b Play Overlapping and Distinct Roles in Mediating Environmental Stress Responses

(2009) J. W. Walley et al.   PLANT PHYSIOLOGY

The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site

(2009) K. R. Andersen et al.   RNA

Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components

(2008) Gemma C Atkinson et al.   BMC EVOLUTIONARY BIOLOGY

Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'

(2008) T. E. Mullen et al.   GENES & DEVELOPMENT

Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates

(2008) Jianli Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

Similar Modes of Interaction Enable Trailer Hitch and EDC3 To Associate with DCP1 and Me31B in Distinct Protein Complexes

(2008) F. Tritschler et al.   MOLECULAR AND CELLULAR BIOLOGY

Degradation of a Polyadenylated rRNA Maturation By-Product Involves One of the Three RRP6-Like Proteins in Arabidopsis thaliana

(2008) H. Lange et al.   MOLECULAR AND CELLULAR BIOLOGY

Lin28 Mediates the Terminal Uridylation of let-7 Precursor MicroRNA

(2008) Inha Heo et al.   MOLECULAR CELL

The Control of mRNA Decapping and P-Body Formation

(2008) Tobias M. Franks et al.   MOLECULAR CELL

Structural Basis of Dcp2 Recognition and Activation by Dcp1

(2008) Meipei She et al.   MOLECULAR CELL

Endonucleolytic RNA cleavage by a eukaryotic exosome

(2008) Alice Lebreton et al.   NATURE

Multifunctional deadenylase complexes diversify mRNA control

(2008) Aaron C. Goldstrohm et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

(2008) Andrea B Eberle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities

(2008) Daneen Schaeffer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolutionary conservation supports ancient origin for Nudt16, a nuclear-localized, RNA-binding, RNA-decapping enzyme

(2008) Melissa J. Taylor et al.   NUCLEIC ACIDS RESEARCH

SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan

(2008) E. Huntzinger et al.   RNA

Deadenylation is a widespread effect of miRNA regulation

(2008) A. Eulalio et al.   RNA