Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants

Emerging Themes in Regulation of Global mRNA Turnover in cis

(2017) Chyi-Ying A. Chen et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2016) Aditya Radhakrishnan et al.   CELL

RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants

(2016) Lin Liu et al.   Molecular Plant

Arabidopsis AtRRP44 has ribonuclease activity that is required to complement the growth defect of yeast rrp44 Mutant

(2016) Naoyoshi Kumakura et al.   Plant Biotechnology

The LSM1-7 Complex Differentially Regulates Arabidopsis Tolerance to Abiotic Stress Conditions by Promoting Selective mRNA Decapping

(2016) Carlos Perea-Resa et al.   PLANT CELL

YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex

(2016) Hao Du et al.   Nature Communications

Sm-Like Protein-Mediated RNA Metabolism Is Required for Heat Stress Tolerance in Arabidopsis

(2016) Masanori Okamoto et al.   Frontiers in Plant Science

EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis

(2015) Wenyang Li et al.   CELL

The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2

(2015) M. E. Roux et al.   EMBO JOURNAL

MicroRNAs in Control of Plant Development

(2015) Chao Li et al.   JOURNAL OF CELLULAR PHYSIOLOGY

In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

(2015) Angel Emilio Martínez de Alba et al.   NUCLEIC ACIDS RESEARCH

SKI2 mediates degradation of RISC 5′-cleavage fragments and prevents secondary siRNA production from miRNA targets inArabidopsis

(2015) Anja Branscheid et al.   NUCLEIC ACIDS RESEARCH

AtCCR4a and AtCCR4b are Involved in Determining the Poly(A) Length of Granule-bound starch synthase 1 Transcript and Modulating Sucrose and Starch Metabolism in Arabidopsis thaliana

(2015) Yuya Suzuki et al.   PLANT AND CELL PHYSIOLOGY

Profiling and Characterization of Small RNAs in the Liverwort,Marchantia polymorpha, Belonging to the First Diverged Land Plants

(2015) Masayuki Tsuzuki et al.   PLANT AND CELL PHYSIOLOGY

Loss of Arabidopsis 5′–3′ Exoribonuclease AtXRN4 Function Enhances Heat Stress Tolerance of Plants Subjected to Severe Heat Stress

(2015) Anh Hai Nguyen et al.   PLANT AND CELL PHYSIOLOGY

Second-Site Mutagenesis of a Hypomorphicargonaute1Allele IdentifiesSUPERKILLER3as an Endogenous Suppressor of Transgene Posttranscriptional Gene Silencing

(2015) Agnès Yu et al.   PLANT PHYSIOLOGY

Suppression of endogenous gene silencing by bidirectional cytoplasmic RNA decay in Arabidopsis

(2015) X. Zhang et al.   SCIENCE

XRN1 Stalling in the 5’ UTR of Hepatitis C Virus and Bovine Viral Diarrhea Virus Is Associated with Dysregulated Host mRNA Stability

(2015) Stephanie L. Moon et al.   PLoS Pathogens

An Rrp6-like Protein Positively Regulates Noncoding RNA Levels and DNA Methylation in Arabidopsis

(2014) Huiming Zhang et al.   MOLECULAR CELL

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Diffuse Decapping Enzyme DCP2 Accumulates in DCP1 Foci Under Heat Stress in Arabidopsis thaliana

(2014) Kazuki Motomura et al.   PLANT AND CELL PHYSIOLOGY

TheArabidopsis thalianatandem zinc finger 1 (AtTZF1) protein in RNA binding and decay

(2014) Jie Qu et al.   PLANT JOURNAL

Role forLSMgenes in the regulation of circadian rhythms

(2014) Soledad Perez-Santángelo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs inArabidopsis

(2014) Mengji Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in Arabidopsis thaliana

(2014) Heike Lange et al.   PLoS Genetics

Arabidopsis RRP6L1 and RRP6L2 Function in FLOWERING LOCUS C Silencing via Regulation of Antisense RNA Synthesis

(2014) Jun-Hye Shin et al.   PLoS Genetics

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

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

(2013) Vinay K. Nagarajan 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

Molecular Insights into microRNA-Mediated Translational Repression in Plants

(2013) Hiro-oki Iwakawa et al.   MOLECULAR CELL

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex

(2013) Debora Lika Makino et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation

(2013) Anna Golisz et al.   NUCLEIC ACIDS RESEARCH

Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants

(2013) Ana Beatriz Moreno et al.   NUCLEIC ACIDS RESEARCH

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

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

Multiple Nudix family proteins possess mRNA decapping activity

(2013) M.-G. Song et al.   RNA

XRN4 and LARP1 Are Required for a Heat-Triggered mRNA Decay Pathway Involved in Plant Acclimation and Survival during Thermal Stress

(2013) Rémy Merret et al.   Cell Reports

Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis

(2012) Virginie Jouannet et al.   EMBO JOURNAL

Dehydration stress activates Arabidopsis MPK6 to signal DCP1 phosphorylation

(2012) Jun Xu et al.   EMBO JOURNAL

Dxo1 is a new type of eukaryotic enzyme with both decapping and 5′-3′ exoribonuclease activity

(2012) Jeong Ho Chang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss of XRN4 Function Can Trigger Cosuppression in a Sequence-Dependent Manner

(2012) Makoto Hayashi et al.   PLANT AND CELL PHYSIOLOGY

RNA Processing Bodies, Peroxisomes, Golgi Bodies, Mitochondria, and Endoplasmic Reticulum Tubule Junctions Frequently Pause at Cortical Microtubules

(2012) Takahiro Hamada et al.   PLANT AND CELL PHYSIOLOGY

miR156 and miR390 Regulate tasiRNA Accumulation and Developmental Timing in Physcomitrella patens

(2012) S. H. Cho et al.   PLANT CELL

LSM Proteins Provide Accurate Splicing and Decay of Selected Transcripts to Ensure Normal Arabidopsis Development

(2012) C. Perea-Resa et al.   PLANT CELL

The ArabidopsisDCP2gene is required for proper mRNA turnover and prevents transgene silencing in Arabidopsis

(2012) Moritz Thran et al.   PLANT JOURNAL

RRP41L, a Putative Core Subunit of the Exosome, Plays an Important Role in Seed Germination and Early Seedling Growth in Arabidopsis

(2012) M. Yang et al.   PLANT PHYSIOLOGY

RDR1 and SGS3, Components of RNA-Mediated Gene Silencing, Are Required for the Regulation of Cuticular Wax Biosynthesis in Developing Inflorescence Stems of Arabidopsis

(2012) P. Lam et al.   PLANT PHYSIOLOGY

Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway

(2012) B. Derrien et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of decapping proteins in the miRNA accumulation inArabidopsis thaliana

(2012) Kazuki Motomura et al.   RNA Biology

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

(2011) Tatjana Trcek et al.   CELL

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

An Importin   Protein Negatively Regulates MicroRNA Activity in Arabidopsis

(2011) W. Wang et al.   PLANT CELL

ArabidopsisFloral Initiator SKB1 Confers High Salt Tolerance by Regulating Transcription and Pre-mRNA Splicing through Altering Histone H4R3 and Small Nuclear Ribonucleoprotein LSM4 Methylation

(2011) Zhaoliang Zhang et al.   PLANT CELL

MTR4, a putative RNA helicase and exosome co-factor, is required for proper rRNA biogenesis and development inArabidopsis thaliana

(2011) Heike Lange et al.   PLANT JOURNAL

The eukaryotic RNA exosome: Same scaffold but variable catalytic subunits

(2011) Søren Lykke-Andersen et al.   RNA Biology

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

RNA Decay and RNA Silencing in Plants: Competition or Collaboration?

(2011) Michael Christie et al.   Frontiers in Plant Science

Multiple mRNA Decapping Enzymes in Mammalian Cells

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

Identification of a quality-control mechanism for mRNA 5′-end capping

(2010) Xinfu Jiao et al.   NATURE

The second face of a known player: Arabidopsis silencing suppressor AtXRN4 acts organ-specifically

(2010) Florian Vogel et al.   NEW PHYTOLOGIST

Conserved RNaseII domain protein functions in cytoplasmic mRNA decay and suppresses Arabidopsis decapping mutant phenotypes

(2010) W. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Fabien Bonneau et al.   CELL

SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6-bodies

(2009) Naoyoshi Kumakura et al.   FEBS LETTERS

Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5′-end stem-loop structures

(2009) You Li 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

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

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

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation

(2008) Taiowa A. Montgomery et al.   CELL

The Arabidopsis homologs of CCR4-associated factor 1 show mRNA deadenylation activity and play a role in plant defence responses

(2008) Wenxing Liang et al.   CELL RESEARCH

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

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

Structure of the Active Subunit of the Yeast Exosome Core, Rrp44: Diverse Modes of Substrate Recruitment in the RNase II Nuclease Family

(2008) Esben Lorentzen et al.   MOLECULAR CELL

Endonucleolytic RNA cleavage by a eukaryotic exosome

(2008) Alice Lebreton et al.   NATURE

The Mechanism Selecting the Guide Strand from Small RNA Duplexes is Different Among Argonaute Proteins

(2008) Atsushi Takeda et al.   PLANT AND CELL PHYSIOLOGY

Plant stress granules and mRNA processing bodies are distinct from heat stress granules

(2008) Christian Weber et al.   PLANT JOURNAL

AGO1-miR173 complex initiates phased siRNA formation in plants

(2008) T. A. Montgomery et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use, tolerance and avoidance of amplified RNA silencing by plants

(2008) Olivier Voinnet   TRENDS IN PLANT SCIENCE