Plant microRNAs: Biogenesis, Homeostasis, and Degradation

MicroRNAs transcriptionally regulate promoter activity in Arabidopsis thaliana

(2019) Guodong Yang et al.   Journal of Integrative Plant Biology

The PROTEIN PHOSPHATASE4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis

(2019) Suikang Wang et al.   PLANT CELL

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

Arabidopsis ARGONAUTE 1 Binds Chromatin to Promote Gene Transcription in Response to Hormones and Stresses

(2018) Chang Liu et al.   DEVELOPMENTAL CELL

Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression

(2018) Zeyang Ma et al.   DEVELOPMENTAL CELL

A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation

(2018) Natalia P. Achkar et al.   DEVELOPMENTAL CELL

Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway

(2018) Nicolas G. Bologna et al.   MOLECULAR CELL

SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis

(2018) Shengjun Li et al.   NUCLEIC ACIDS RESEARCH

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides

(2018) Bala Ani Akpinar et al.   PLANT BIOTECHNOLOGY JOURNAL

Biogenesis and regulatory hierarchy of phased small interfering RNAs in plants

(2018) Pingchuan Deng et al.   PLANT BIOTECHNOLOGY JOURNAL

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

(2018) Michael J. Axtell et al.   PLANT CELL

Degradation of unmethylated miRNA/miRNA*s by a DEDDy-type 3′ to 5′ exoribonuclease Atrimmer 2 inArabidopsis

(2018) Xiaoyan Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant Small Non-coding RNAs and Their Roles in Biotic Stresses

(2018) Eleanor J. Brant et al.   Frontiers in Plant Science

SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production

(2018) Zhiye Wang et al.   NATURE

Regulation of microRNA biogenesis and its crosstalk with other cellular pathways

(2018) Thomas Treiber et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural and biochemical insights into small RNA 3′ end trimming by Arabidopsis SDN1

(2018) Jiayi Chen et al.   Nature Communications

Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes

(2018) Corinna Speth et al.   eLife

piRNA-Guided Genome Defense: From Biogenesis to Silencing

(2018) Benjamin Czech et al.   Annual Review of Genetics

The F-box protein HAWAIIAN SKIRT is required for mimicry target induced microRNA degradation in Arabidopsis

(2018) Jun Mei et al.   Journal of Integrative Plant Biology

Iruka Eliminates Dysfunctional Argonaute by Selective Ubiquitination of Its Empty State

(2018) Hotaka Kobayashi et al.   MOLECULAR CELL

The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs

(2018) Qiang Cai et al.   Nature Communications

Respective Contributions of URT1 and HESO1 to the Uridylation of 5′ Fragments Produced From RISC-Cleaved mRNAs

(2018) Hélène Zuber et al.   Frontiers in Plant Science

An Argonaute phosphorylation cycle promotes microRNA-mediated silencing

(2017) Ryan J. Golden et al.   NATURE

The ‘how’ and ‘where’ of plant microRNAs

(2017) Yu Yu et al.   NEW PHYTOLOGIST

The functions of plant small RNAs in development and in stress responses

(2017) Shengjun Li et al.   PLANT JOURNAL

A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function

(2017) Patricia L. M. Lang et al.   PLANT PHYSIOLOGY

KETCH1 imports HYL1 to nucleus for miRNA biogenesis inArabidopsis

(2017) Zhonghui Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tudor-SN–mediated endonucleolytic decay of human cell microRNAs promotes G1/S phase transition

(2017) Reyad A. Elbarbary et al.   SCIENCE

Transfer RNA-derived small RNAs in plants

(2017) Lei Zhu et al.   Science China-Life Sciences

ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis

(2017) Yu Yu et al.   PLOS BIOLOGY

The SnRK2 kinases modulate miRNA accumulation in Arabidopsis

(2017) Jun Yan et al.   PLoS Genetics

RISC-interacting clearing 3’- 5’ exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana

(2017) Zhonghui Zhang et al.   eLife

Polycomb Group Proteins RING1A and RING1B Regulate the Vegetative Phase Transition in Arabidopsis

(2017) Jian Li et al.   Frontiers in Plant Science

The evolutionary origin of plant and animal microRNAs

(2017) Yehu Moran et al.   Nature Ecology & Evolution

The RNase PARN-1 Trims piRNA 3′ Ends to Promote Transcriptome Surveillance in C. elegans

(2016) Wen Tang et al.   CELL

Identification and Functional Analysis of the Pre-piRNA 3′ Trimmer in Silkworms

(2016) Natsuko Izumi et al.   CELL

Class III HD-ZIPs govern vascular cell fate: an HD view on patterning and differentiation

(2016) Prashanth Ramachandran et al.   JOURNAL OF EXPERIMENTAL BOTANY

Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs

(2016) Anna Łabno et al.   NUCLEIC ACIDS RESEARCH

RNAi in Plants: An Argonaute-Centered View

(2016) Xiaofeng Fang et al.   PLANT CELL

TRANSPORTIN1 Promotes the Association of MicroRNA with ARGONAUTE1 in Arabidopsis

(2016) Yuwei Cui et al.   PLANT CELL

Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels

(2016) Jakub Dolata et al.   PLANT PHYSIOLOGY

miRNA863-3p sequentially targets negative immune regulator ARLPKs and positive regulator SERRATE upon bacterial infection

(2016) Dongdong Niu et al.   Nature Communications

Dis3l2-Mediated Decay Is a Quality Control Pathway for Noncoding RNAs

(2016) Mehdi Pirouz et al.   Cell Reports

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

(2016) Varsha Shriram et al.   Frontiers in Plant Science

Antiviral roles of plant ARGONAUTES

(2015) Alberto Carbonell et al.   CURRENT OPINION IN PLANT BIOLOGY

Evolution, functions, and mysteries of plant ARGONAUTE proteins

(2015) Han Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

Potent degradation of neuronal miRNAs induced by highly complementary targets

(2015) M. de la Mata et al.   EMBO REPORTS

Plant miRNAs: biogenesis, organization and origins

(2015) Hikmet Budak et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

CMA33/XCT Regulates Small RNA Production through Modulating the Transcription of Dicer-Like Genes in Arabidopsis

(2015) Xiaofeng Fang et al.   Molecular Plant

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic Regulation of Vegetative Phase Change in Arabidopsis

(2015) Mingli Xu et al.   PLANT CELL

Stress responsive miRNAs and isomiRs in cereals

(2015) Hikmet Budak et al.   PLANT SCIENCE

KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1

(2015) Patricia Karlsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Post-transcriptional gene silencing in plants: a double-edged sword

(2015) Xinyan Zhang et al.   Science China-Life Sciences

The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs

(2015) Zhenfei Sun et al.   PLoS Genetics

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

New insights into pri-miRNA processing and accumulation in plants

(2015) Shuxin Zhang et al.   Wiley Interdisciplinary Reviews-RNA

MicroRNA Promoter Identification inArabidopsisUsing Multiple Histone Markers

(2015) Yuming Zhao et al.   Biomed Research International

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis

(2015) Xiaofeng Fang et al.   Nature Plants

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

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

MicroRNA biogenesis factor DRB1 is a phosphorylation target of mitogen activated protein kinase MPK3 in both rice and Arabidopsis

(2014) Badmi Raghuram et al.   FEBS Journal

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

The evolutionary journey of Argonaute proteins

(2014) Daan C Swarts et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA

(2014) Xi Yang et al.   NUCLEIC ACIDS RESEARCH

HUA ENHANCER1 Is Involved in Posttranscriptional Regulation of Positive and Negative Regulators inArabidopsisPhotomorphogenesis

(2014) Huang-Lung Tsai et al.   PLANT CELL

Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots

(2014) D. Muraro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Small RNAs meet their targets: When methylation defends miRNAs from uridylation

(2014) Guodong Ren et al.   RNA Biology

COP1 E3 ligase protects HYL1 to retain microRNA biogenesis

(2014) Seok Keun Cho et al.   Nature Communications

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Multiple RNA recognition patterns during microRNA biogenesis in plants

(2013) N. G. Bologna et al.   GENOME RESEARCH

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

(2013) Hao-Ming Chang et al.   NATURE

Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

(2013) Hongliang Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara 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

NOT2 Proteins Promote Polymerase II-Dependent Transcription and Interact with Multiple MicroRNA Biogenesis Factors in Arabidopsis

(2013) L. Wang et al.   PLANT CELL

Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs

(2013) K. Rogers et al.   PLANT CELL

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

Complementation of Hyponastic Leaves1 by Double-Strand RNA-Binding Domains of Dicer-Like1 in Nuclear Dicing Bodies

(2013) Q. Liu et al.   PLANT PHYSIOLOGY

CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts

(2013) S. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

(2012) Pablo A. Manavella 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

Origins and Evolution of MicroRNA Genes in Plant Species

(2012) Masafumi Nozawa et al.   Genome Biology and Evolution

STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis

(2012) Samir Ben Chaabane et al.   NUCLEIC ACIDS RESEARCH

Effective Small RNA Destruction by the Expression of a Short Tandem Target Mimic in Arabidopsis

(2012) J. Yan et al.   PLANT CELL

Failure of the Tomato Trans-Acting Short Interfering RNA Program to Regulate AUXIN RESPONSE FACTOR3 and ARF4 Underlies the Wiry Leaf Syndrome

(2012) T. Yifhar et al.   PLANT CELL

CDKF;1 and CDKD Protein Kinases Regulate Phosphorylation of Serine Residues in the C-Terminal Domain ofArabidopsisRNA Polymerase II

(2012) Mohsen Hajheidari et al.   PLANT CELL

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

(2012) A. Carbonell et al.   PLANT CELL

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production

(2012) Chongyuan Luo et al.   PLANT JOURNAL

The Helicase and RNaseIIIa Domains of Arabidopsis Dicer-Like1 Modulate Catalytic Parameters during MicroRNA Biogenesis

(2012) C. Liu et al.   PLANT PHYSIOLOGY

Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis

(2012) G. Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2011) Hongliang Zhu et al.   CELL

The Exoribonuclease Nibbler Controls 3′ End Processing of MicroRNAs in Drosophila

(2011) Nan Liu et al.   CURRENT BIOLOGY

The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1

(2011) Bo W. Han et al.   CURRENT BIOLOGY

The role of Mediator in small and long noncoding RNA production inArabidopsis thaliana

(2011) Yun Ju Kim et al.   EMBO JOURNAL

Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants

(2011) Taichiro Iki et al.   EMBO JOURNAL

Binding of the Cyclophilin 40 Ortholog SQUINT to Hsp90 Protein Is Required for SQUINT Function inArabidopsis

(2011) Keith W. Earley et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2011) Xiaoming Zhang et al.   MOLECULAR CELL

An Importin   Protein Negatively Regulates MicroRNA Activity in Arabidopsis

(2011) W. Wang et al.   PLANT CELL

Hsc70/Hsp90 Chaperone Machinery Mediates ATP-Dependent RISC Loading of Small RNA Duplexes

(2010) Shintaro Iwasaki et al.   MOLECULAR CELL

In Vitro Assembly of Plant RNA-Induced Silencing Complexes Facilitated by Molecular Chaperone HSP90

(2010) Taichiro Iki et al.   MOLECULAR CELL

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

The silencing suppressor P25 of Potato virus X interacts with Argonaute1 and mediates its degradation through the proteasome pathway

(2010) MENG-HSUEN CHIU et al.   MOLECULAR PLANT PATHOLOGY

Polerovirus protein P0 prevents the assembly of small RNA-containing RISC complexes and leads to degradation of ARGONAUTE1

(2010) Tibor Csorba et al.   PLANT JOURNAL

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

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

Differential regulation of microRNA stability

(2010) S. Bail et al.   RNA

Target RNA-Directed Trimming and Tailing of Small Silencing RNAs

(2010) S. L. Ameres et al.   SCIENCE

Structure of Arabidopsis HYPONASTIC LEAVES1 and Its Molecular Implications for miRNA Processing

(2010) Seong Wook Yang et al.   STRUCTURE

A Collection of Target Mimics for Comprehensive Analysis of MicroRNA Function in Arabidopsis thaliana

(2010) Marco Todesco et al.   PLoS Genetics

Histone acetyltransferase GCN5 interferes with the miRNA pathway in Arabidopsis

(2009) Wanhui Kim et al.   CELL RESEARCH

Identification of MicroRNA Processing Determinants by Random Mutagenesis of Arabidopsis MIR172a Precursor

(2009) Julieta L. Mateos et al.   CURRENT BIOLOGY

RNA Secondary Structural Determinants of miRNA Precursor Processing in Arabidopsis

(2009) Liang Song et al.   CURRENT BIOLOGY

Structure Determinants for Accurate Processing of miR172a in Arabidopsis thaliana

(2009) Schallum Werner et al.   CURRENT BIOLOGY

A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159

(2009) Nicolás G Bologna et al.   EMBO JOURNAL

Active turnover modulates mature microRNA activity in Caenorhabditis elegans

(2009) Saibal Chatterjee et al.   NATURE

Adenylation of plant miRNAs

(2009) S. Lu et al.   NUCLEIC ACIDS RESEARCH

Cyclophilin 40 is required for microRNA activity in Arabidopsis

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

A dominant mutation in DCL1 suppresses the hyl1 mutant phenotype by promoting the processing of miRNA

(2009) Y. Tagami et al.   RNA

Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome

(2009) C. Addo-Quaye et al.   RNA

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

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

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

The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1

(2008) Z. Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Degradation of microRNAs by a Family of Exoribonucleases in Arabidopsis

(2008) Vanitharani Ramachandran et al.   SCIENCE

SINE RNA Induces Severe Developmental Defects in Arabidopsis thaliana and Interacts with HYL1 (DRB1), a Key Member of the DCL1 Complex

(2008) Marie-Noëlle Pouch-Pélissier et al.   PLoS Genetics