Structural and molecular mechanisms for the control of eukaryotic 5′–3′ mRNA decay

P-Bodies: Composition, Properties, and Functions

(2018) Yang Luo et al.   BIOCHEMISTRY

Phase Transitions in the Assembly and Function of Human miRISC

(2018) Jessica Sheu-Gruttadauria et al.   CELL

RNA tales – how embryos read and discard messages from mom

(2018) Vladimir Despic et al.   JOURNAL OF CELL SCIENCE

mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases

(2018) Michael W. Webster et al.   MOLECULAR CELL

PABP Cooperates with the CCR4-NOT Complex to Promote mRNA Deadenylation and Block Precocious Decay

(2018) Hyerim Yi et al.   MOLECULAR CELL

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Control of mRNA decapping by autoinhibition

(2018) David R Paquette et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Cinthia C Amaya Ramirez et al.   NUCLEIC ACIDS RESEARCH

Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells

(2018) Pamela Nicholson et al.   RNA

The m6A reader protein YTHDC2 interacts with the small ribosomal subunit and the 5′-3′ exoribonuclease XRN1

(2018) Jens Kretschmer et al.   RNA

Eukaryotic RNA 5′-End NAD + Capping and DeNADding

(2018) Megerditch Kiledjian   TRENDS IN CELL BIOLOGY

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

Mechanistic Insights into MicroRNA-Mediated Gene Silencing

(2018) Thomas F. Duchaine et al.   Cold Spring Harbor Perspectives in Biology

Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis

(2018) Jeffrey S. Mugridge et al.   Nature Communications

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Context-dependent deposition and regulation of mRNAs in P-bodies

(2018) Congwei Wang et al.   eLife

Codon usage bias controls mRNA and protein abundance in trypanosomatids

(2018) Laura Jeacock et al.   eLife

Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability

(2018) Leon Y Chan et al.   eLife

Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway

(2018) Srivathsan Adivarahan et al.   MOLECULAR CELL

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors

(2017) John C. Zinder et al.   GENES & DEVELOPMENT

P-Body Purification Reveals the Condensation of Repressed mRNA Regulons

(2017) Arnaud Hubstenberger et al.   MOLECULAR CELL

The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells

(2017) Ivana Horvathova et al.   MOLECULAR CELL

An improved MS2 system for accurate reporting of the mRNA life cycle

(2017) Evelina Tutucci et al.   NATURE METHODS

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A synergistic network of interactions promotes the formation of in vitro processing bodies and protects mRNA against decapping

(2017) Stefan Schütz et al.   NUCLEIC ACIDS RESEARCH

A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5′–3′ mRNA exonuclease in yeast

(2017) Clément Charenton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme

(2017) Jan Philip Wurm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drosophila Bag-of-marbles directly interacts with the CAF40 subunit of the CCR4–NOT complex to elicit repression of mRNA targets

(2017) Annamaria Sgromo et al.   RNA

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA uridylation: a key posttranscriptional modification shaping the coding and noncoding transcriptome

(2017) Caroline De Almeida et al.   Wiley Interdisciplinary Reviews-RNA

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe

(2016) Yuriko Harigaya et al.   BMC GENOMICS

The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality

(2016) Aditya Radhakrishnan et al.   CELL

Distinct modes of recruitment of the CCR4–NOT complex byDrosophilaand vertebrate Nanos

(2016) Tobias Raisch et al.   EMBO JOURNAL

Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

Connections Underlying Translation and mRNA Stability

(2016) Aditya Radhakrishnan et al.   JOURNAL OF MOLECULAR BIOLOGY

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

(2016) Yuichiro Mishima et al.   MOLECULAR CELL

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

Structure of the active form of Dcp1–Dcp2 decapping enzyme bound to m7GDP and its Edc3 activator

(2016) Clément Charenton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of the Dcp2–Dcp1 mRNA-decapping complex in the activated conformation

(2016) Eugene Valkov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of mRNA-cap recognition by Dcp1–Dcp2

(2016) Jeffrey S Mugridge et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis

(2016) Xiang Yu et al.   PLANT CELL

The cryo-EM structure of a ribosome–Ski2-Ski3-Ski8 helicase complex

(2016) Christian Schmidt et al.   SCIENCE

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex

(2016) Marta Ukleja et al.   Nature Communications

Structure of the active form of Dcp1–Dcp2 decapping enzyme bound to m7GDP and its Edc3 activator

(2016) Clément Charenton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of the Dcp2–Dcp1 mRNA-decapping complex in the activated conformation

(2016) Eugene Valkov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of mRNA-cap recognition by Dcp1–Dcp2

(2016) Jeffrey S Mugridge et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1

(2016) James A.W. Stowell et al.   Cell Reports

New insights into decapping enzymes and selective mRNA decay

(2016) Ewa Grudzien-Nogalska et al.   Wiley Interdisciplinary Reviews-RNA

Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact

(2016) Evangelos D. Karousis et al.   Wiley Interdisciplinary Reviews-RNA

The Ccr4-Not complex is a key regulator of eukaryotic gene expression

(2016) Martine A. Collart   Wiley Interdisciplinary Reviews-RNA

Cotranslational microRNA mediated messenger RNA destabilization

(2016) Trinh To Tat et al.   eLife

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

(2015) Vicent Pelechano et al.   CELL

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Towards a molecular understanding of microRNA-mediated gene silencing

(2015) Stefanie Jonas et al.   NATURE REVIEWS GENETICS

Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes

(2015) Søren Lykke-Andersen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Control of mRNA decapping by positive and negative regulatory elements in the Dcp2 C-terminal domain

(2015) Feng He et al.   RNA

Emerging roles for RNA degradation in viral replication and antiviral defense

(2015) Emma Abernathy et al.   VIROLOGY

Structure of a Human 4E-T/DDX6/CNOT1 Complex Reveals the Different Interplay of DDX6-Binding Proteins with the CCR4-NOT Complex

(2015) Sevim Ozgur et al.   Cell Reports

In Vitro Reconstitution of a Cellular Phase-Transition Process that Involves the mRNA Decapping Machinery

(2014) Simon A. Fromm et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

mRNA deadenylation by Pan2–Pan3: Figure 1

(2014) Jana Wolf et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Poly(A)-binding proteins are required for diverse biological processes in metazoans

(2014) Richard W.P. Smith et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation

(2014) J. Wolf et al.   EMBO JOURNAL

Yeast Edc3 Targets RPS28B mRNA for Decapping by Binding to a 3' Untranslated Region Decay-Inducing Regulatory Element

(2014) F. He et al.   MOLECULAR AND CELLULAR BIOLOGY

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

A DDX6-CNOT1 Complex and W-Binding Pockets in CNOT9 Reveal Direct Links between miRNA Target Recognition and Silencing

(2014) Ying Chen et al.   MOLECULAR CELL

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

The structure of the Pan2–Pan3 core complex reveals cross-talk between deadenylase and pseudokinase

(2014) Ingmar B Schäfer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An asymmetric PAN3 dimer recruits a single PAN2 exonuclease to mediate mRNA deadenylation and decay

(2014) Stefanie Jonas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1

(2014) Chung-Te Chang et al.   NUCLEIC ACIDS RESEARCH

Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain

(2014) S. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

XRN 5′→3′ exoribonucleases: Structure, mechanisms and functions

(2013) Vinay K. Nagarajan et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The DHH1/RCKp54 family of helicases: An ancient family of proteins that promote translational silencing

(2013) Vlad Presnyak et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs

(2013) Alex Charles Tuck 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

The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2

(2013) B. Loh et al.   GENES & DEVELOPMENT

The role of disordered protein regions in the assembly of decapping complexes and RNP granules

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

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

(2013) Mai Sun et al.   MOLECULAR CELL

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Structural basis for the recruitment of the human CCR4–NOT deadenylase complex by tristetraprolin

(2013) Marc R Fabian et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay

(2013) Olga Kolesnikova et al.   NUCLEIC ACIDS RESEARCH

Structural analysis of the yeast Dhh1–Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions

(2013) Humayun Sharif et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Humayun Sharif et al.   Cell Reports

Structural and functional control of the eukaryotic mRNA decapping machinery

(2012) Marcos Arribas-Layton et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA Degradation in Saccharomyces cerevisae

(2012) Roy Parker   GENETICS

Dcp2 Decapping Protein Modulates mRNA Stability of the Critical Interferon Regulatory Factor (IRF) IRF-7

(2012) Y. Li et al.   MOLECULAR AND CELLULAR BIOLOGY

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

Interdomain dynamics and coactivation of the mRNA decapping enzyme Dcp2 are mediated by a gatekeeper tryptophan

(2012) S. N. Floor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis of the PNRC2-Mediated Link between mRNA Surveillance and Decapping

(2012) Tingfeng Lai et al.   STRUCTURE

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

(2011) Simon A Fromm et al.   EMBO JOURNAL

GW182 Proteins Directly Recruit Cytoplasmic Deadenylase Complexes to miRNA Targets

(2011) Joerg E. Braun et al.   MOLECULAR CELL

miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4–NOT

(2011) Marc R Fabian et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cytoplasmic deadenylation: regulation of mRNA fate

(2010) Katrin Wiederhold et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Decapping Activators in Saccharomyces cerevisiae Act by Multiple Mechanisms

(2010) Tracy Nissan et al.   MOLECULAR CELL

Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition

(2010) M. S. Borja et al.   RNA

Human Proline-Rich Nuclear Receptor Coregulatory Protein 2 Mediates an Interaction between mRNA Surveillance Machinery and Decapping Complex

(2009) Hana Cho et al.   MOLECULAR CELL

Co-translational mRNA decay in Saccharomyces cerevisiae

(2009) Wenqian Hu et al.   NATURE

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

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

BTG/TOB factors impact deadenylases

(2009) Fabienne Mauxion et al.   TRENDS IN BIOCHEMICAL SCIENCES

mRNA Decapping Is Promoted by an RNA-Binding Channel in Dcp2

(2008) Mandar V. Deshmukh et al.   MOLECULAR CELL

Structural Basis of Dcp2 Recognition and Activation by Dcp1

(2008) Meipei She et al.   MOLECULAR CELL