The expanding world of small RNAs in plants

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

Epigenetic transitions leading to heritable, RNA-mediated de novo silencing inArabidopsis thaliana

(2015) Donna M. Bond et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) X. Zhang et al.   SCIENCE

Synergistic and Independent Actions of Multiple Terminal Nucleotidyl Transferases in the 3’ Tailing of Small RNAs in Arabidopsis

(2015) Xiaoyan Wang et al.   PLoS Genetics

Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in Arabidopsis

(2015) Bin Tu et al.   PLoS Genetics

The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs inArabidopsis

(2014) Nicolas G. Bologna et al.   Annual Review of Plant Biology

The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing

(2014) Zhao Zhang et al.   CELL

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Generation of transgenic golden Syrian hamsters

(2014) Mingming Gao et al.   CELL RESEARCH

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation

(2014) A. D. McCue et al.   EMBO JOURNAL

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale inArabidopsisreveals features and regulation of siRNA biogenesis

(2014) Shaofang Li et al.   GENOME RESEARCH

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

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

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

Small RNAs break out: the molecular cell biology of mobile small RNAs

(2014) Peter Sarkies et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Thedicer-like1Homologfuzzy tasselIs Required for the Regulation of Meristem Determinacy in the Inflorescence and Vegetative Growth in Maize

(2014) Beth E. Thompson et al.   PLANT CELL

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

(2014) Siwaret Arikit et al.   PLANT CELL

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs

(2014) Reina Komiya et al.   PLANT JOURNAL

Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing

(2014) Jean-Sébastien Parent et al.   PLANT JOURNAL

Comparative expression profiling of miRNAs between the cytoplasmic male sterile line MeixiangA and its maintainer line MeixiangB during rice anther development

(2014) Junjie Yan et al.   PLANTA

Methylation protects microRNAs from an AGO1-associated activity that uridylates 5' RNA fragments generated by AGO1 cleavage

(2014) G. Ren 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

ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis

(2014) Xiaoming Zhang et al.   Nature Communications

The Proper Splicing of RNAi Factors Is Critical for Pericentric Heterochromatin Assembly in Fission Yeast

(2014) Scott P. Kallgren et al.   PLoS Genetics

On the role of some ARGONAUTE proteins in meiosis and DNA repair in Arabidopsis thaliana

(2014) Cecilia Oliver et al.   Frontiers in Plant Science

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

Stalled Spliceosomes Are a Signal for RNAi-Mediated Genome Defense

(2013) Phillip A. Dumesic et al.   CELL

Biogenesis and function of rice small RNAs from non-coding RNA precursors

(2013) Siwaret Arikit et al.   CURRENT OPINION IN PLANT BIOLOGY

RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis

(2013) T. M. Vu et al.   DEVELOPMENT

Protection of Germline Gene Expression by the C. elegans Argonaute CSR-1

(2013) Christopher J. Wedeles et al.   DEVELOPMENTAL CELL

Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly

(2013) Yayoi Endo et al.   EMBO REPORTS

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Genomic and epigenetic insights into the molecular bases of heterosis

(2013) Z. Jeffrey Chen   NATURE REVIEWS GENETICS

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

The contribution of pseudouridine to stabilities and structure of RNAs

(2013) Elzbieta Kierzek et al.   NUCLEIC ACIDS RESEARCH

The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana

(2013) K. D. Raczynska et al.   NUCLEIC ACIDS RESEARCH

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

Plant MicroRNAs Display Differential 3' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species

(2013) J. Zhai et al.   PLANT CELL

Lessons on RNA Silencing Mechanisms in Plants from Eukaryotic Argonaute Structures

(2013) Christian Poulsen et al.   PLANT CELL

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs

(2013) S. Nuthikattu et al.   PLANT PHYSIOLOGY

HAMR: high-throughput annotation of modified ribonucleotides

(2013) P. Ryvkin et al.   RNA

The role of epigenetics in hybrid vigour

(2013) Michael Groszmann et al.   TRENDS IN GENETICS

Specific Tandem Repeats Are Sufficient for Paramutation-Induced Trans-Generational Silencing

(2013) Christiane L. Belele et al.   PLoS Genetics

Polyploids as a “model system” for the study of heterosis

(2013) Jacob D. Washburn et al.   Plant Reproduction

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

(2012) Jiamu Du et al.   CELL

piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline

(2012) Masaki Shirayama et al.   CELL

A Role for Small RNAs in DNA Double-Strand Break Repair

(2012) Wei Wei 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

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis

(2012) Guodong Ren et al.   CURRENT BIOLOGY

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

(2012) Yuanyuan Zhao et al.   CURRENT BIOLOGY

Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation

(2012) Stéphanie Durand et al.   CURRENT BIOLOGY

Paramutation: a trans-homolog interaction affecting heritable gene regulation

(2012) Jay B Hollick   CURRENT OPINION IN PLANT BIOLOGY

Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility

(2012) Danny W-K Ng et al.   CURRENT OPINION IN PLANT BIOLOGY

Somatic small RNA pathways promote the mitotic events of megagametogenesis during female reproductive development in Arabidopsis

(2012) M. R. Tucker et al.   DEVELOPMENT

ArabidopsisArgonaute MID domains use their nucleotide specificity loop to sort small RNAs

(2012) Filipp Frank et al.   EMBO JOURNAL

The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis

(2012) Israel Ausin et al.   Epigenetics

Evolution of Animal and Plant Dicers: Early Parallel Duplications and Recurrent Adaptation of Antiviral RNA Binding in Plants

(2012) Krishanu Mukherjee et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNAi triggered by specialized machinery silences developmental genes and retrotransposons

(2012) Soichiro Yamanaka et al.   NATURE

Site-specific DICER and DROSHA RNA products control the DNA-damage response

(2012) Sofia Francia et al.   NATURE

A small RNA response at DNA ends in Drosophila

(2012) Katharina M. Michalik et al.   NUCLEIC ACIDS RESEARCH

A MicroRNA Superfamily Regulates Nucleotide Binding Site-Leucine-Rich Repeats and Other mRNAs

(2012) P. V. Shivaprasad et al.   PLANT CELL

Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

(2012) H. Shen 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

Plant secondary siRNA production determined by microRNA-duplex structure

(2012) P. A. Manavella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeat associated small RNAs vary among parents and following hybridization in maize

(2012) W. T. Barber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

(2012) Andrea D. McCue et al.   PLoS Genetics

Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair

(2011) Irene Chiolo et al.   CELL

Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development

(2011) Hongliang Zhu et al.   CELL

The Inside-Out Mechanism of Dicers from Budding Yeasts

(2011) David E. Weinberg et al.   CELL

Plant small RNAs as morphogens

(2011) Damianos S Skopelitis et al.   CURRENT OPINION IN CELL BIOLOGY

Paramutation: a process for acquiring trans-generational regulatory states

(2011) Karl F Erhard et al.   CURRENT OPINION IN PLANT BIOLOGY

Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs

(2011) Padubidri V Shivaprasad et al.   EMBO JOURNAL

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

(2011) S. K. Wyman et al.   GENOME RESEARCH

MicroRNA activity in the Arabidopsis male germline

(2011) Filipe Borges et al.   JOURNAL OF EXPERIMENTAL BOTANY

Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393∗-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12

(2011) Xiaoming Zhang et al.   MOLECULAR CELL

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II

(2011) Mikel Zaratiegui et al.   NATURE

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

(2011) Jeremy R. Haag et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

The 21-Nucleotide, but Not 22-Nucleotide, Viral Secondary Small Interfering RNAs Direct Potent Antiviral Defense by Two Cooperative Argonautes inArabidopsis thaliana

(2011) Xian-Bing Wang et al.   PLANT CELL

Production of Viable Gametes without Meiosis in Maize Deficient for an ARGONAUTE Protein

(2011) Manjit Singh et al.   PLANT CELL

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

(2011) Xianwei Song et al.   PLANT JOURNAL

Intron splicing suppresses RNA silencing in Arabidopsis

(2011) Michael Christie et al.   PLANT JOURNAL

Evolution of MicroRNA Genes in Oryza sativa and Arabidopsis thaliana: An Update of the Inverted Duplication Model

(2011) Yun Zhang et al.   PLoS One

ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two MicroRNAs in Arabidopsis

(2011) Lijuan Ji et al.   PLoS Genetics

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

(2011) Michael J Axtell et al.   GENOME BIOLOGY

Modifications of Small RNAs and Their Associated Proteins

(2010) Young-Kook Kim et al.   CELL

Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis

(2010) M. Ron et al.   GENES & DEVELOPMENT

MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis

(2010) M. D. Nodine et al.   GENES & DEVELOPMENT

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate

(2010) Annelie Carlsbecker et al.   NATURE

Control of female gamete formation by a small RNA pathway in Arabidopsis

(2010) Vianey Olmedo-Monfil et al.   NATURE

Small RNA sorting: matchmaking for Argonautes

(2010) Benjamin Czech et al.   NATURE REVIEWS GENETICS

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

siRNAs from miRNA sites mediate DNA methylation of target genes

(2010) Padmanabhan Chellappan et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Gene Evolution inArabidopsis lyrataandArabidopsis thaliana

(2010) Noah Fahlgren et al.   PLANT CELL

The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci

(2010) E. R. Havecker et al.   PLANT CELL

Arabidopsis RNA-Dependent RNA Polymerases and Dicer-Like Proteins in Antiviral Defense and Small Interfering RNA Biogenesis during Turnip Mosaic Virus Infection

(2010) H. Garcia-Ruiz et al.   PLANT CELL

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

Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells

(2010) A. Molnar et al.   SCIENCE

Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana

(2009) Kei Iida et al.   BMC GENOMICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

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

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

TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation

(2009) Inha Heo et al.   CELL

Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173

(2009) Felipe F Felippes et al.   EMBO REPORTS

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

(2009) Naoyoshi Kumakura et al.   FEBS LETTERS

Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups

(2009) Jie Zong et al.   GENE

Pattern formation via small RNA mobility

(2009) D. H. Chitwood et al.   GENES & DEVELOPMENT

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

Involvement of the Spliceosomal U4 Small Nuclear RNA in Heterochromatic Gene Silencing at Fission Yeast Centromeres

(2009) Madoka Chinen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Splicing Factor Spf30 Assists Exosome-Mediated Gene Silencing in Fission Yeast

(2009) P. Bernard et al.   MOLECULAR AND CELLULAR BIOLOGY

qiRNA is a new type of small interfering RNA induced by DNA damage

(2009) Heng-Chi Lee et al.   NATURE

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

(2009) Rebecca A. Mosher et al.   NATURE

Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells

(2009) John P Hagan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications

(2009) H. Alexander Ebhardt et al.   NUCLEIC ACIDS RESEARCH

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana

(2009) X.-B. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice

(2008) Meenu Kapoor et al.   BMC GENOMICS

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

RNA Interference Guides Histone Modification during the S Phase of Chromosomal Replication

(2008) Anna Kloc et al.   CURRENT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

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

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

(2008) B. Ben Amor et al.   GENOME RESEARCH

Evolution of Arabidopsis MIR genes generates novel microRNA classes

(2008) Franck Vazquez et al.   NUCLEIC ACIDS RESEARCH

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

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

The ARGONAUTE10 gene modulates shoot apical meristem maintenance and establishment of leaf polarity by repressing miR165/166 in Arabidopsis

(2008) Qili Liu et al.   PLANT JOURNAL

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

(2008) S. Laubinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual coding of siRNAs and miRNAs by plant transposable elements

(2008) J. Piriyapongsa et al.   RNA

Splicing Factors Facilitate RNAi-Directed Silencing in Fission Yeast

(2008) E. H. Bayne et al.   SCIENCE

Degradation of microRNAs by a Family of Exoribonucleases in Arabidopsis

(2008) Vanitharani Ramachandran et al.   SCIENCE

Epigenomic Consequences of Immortalized Plant Cell Suspension Culture

(2008) Milos Tanurdzic et al.   PLOS BIOLOGY