RNA-based regulation of transposon expression

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

(2015) Kirsten-André Senti et al.   GENES & DEVELOPMENT

Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline

(2015) Kaoru Sato et al.   MOLECULAR CELL

Small-RNA-Mediated Genome-wide trans -Recognition Network in Tetrahymena DNA Elimination

(2015) Tomoko Noto et al.   MOLECULAR CELL

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

(2015) Benoît Piégu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance inArabidopsis

(2015) Xuehua Zhong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tupaia small RNAs provide insights into function and evolution of RNAi-based transposon defense in mammals

(2015) David Rosenkranz et al.   RNA

piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis

(2015) F. Mohn et al.   SCIENCE

piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production

(2015) B. W. Han et al.   SCIENCE

PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis

(2015) David Homolka et al.   Cell Reports

Piwi Proteins and piRNAs in Mammalian Oocytes and Early Embryos

(2015) Elke F. Roovers et al.   Cell Reports

MicroRNA-Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells

(2015) Bruno Mugat et al.   PLoS Genetics

Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity

(2014) Mart Krupovic et al.   BMC BIOLOGY

Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases

(2014) Xuehua Zhong et al.   CELL

RNA Clamping by Vasa Assembles a piRNA Amplifier Complex on Transposon Transcripts

(2014) Jordi Xiol et al.   CELL

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

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

Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation

(2014) C.-G. Duan et al.   EMBO JOURNAL

piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells

(2014) D. Pezic et al.   GENES & DEVELOPMENT

The Initial Uridine of Primary piRNAs Does Not Create the Tenth Adenine that Is the Hallmark of Secondary piRNAs

(2014) Wei Wang et al.   MOLECULAR CELL

CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity

(2014) Rodolphe Barrangou et al.   MOLECULAR CELL

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

Evolution of adaptive immunity from transposable elements combined with innate immune systems

(2014) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing

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

The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs

(2014) E. Cora et al.   RNA

The SET Domain Proteins SUVH2 and SUVH9 Are Required for Pol V Occupancy at RNA-Directed DNA Methylation Loci

(2014) Zhang-Wei Liu et al.   PLoS Genetics

Tn5 transposition in Escherichia coli is repressed by Hfq and activated by over-expression of the small non-coding RNA SgrS

(2014) Joseph A Ross et al.   Mobile DNA

CRISPR-Cas immunity and mobile DNA: a new superfamily of DNA transposons encoding a Cas1 endonuclease

(2014) Alison B Hickman et al.   Mobile DNA

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Mtr4-like Protein Coordinates Nuclear RNA Processing for Heterochromatin Assembly and for Telomere Maintenance

(2013) Nathan N. Lee et al.   CELL

Stalled Spliceosomes Are a Signal for RNAi-Mediated Genome Defense

(2013) Phillip A. Dumesic et al.   CELL

A Retrotransposon-Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes

(2013) Matyas Flemr et al.   CELL

The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles

(2013) A. K. Lim et al.   DEVELOPMENT

A Major Epigenetic Programming Mechanism Guided by piRNAs

(2013) Xiao A. Huang et al.   DEVELOPMENTAL CELL

Expression ofPorphyromonas gingivalissmall RNA in response to hemin availability identified using microarray and RNA-seq analysis

(2013) Priscilla Phillips et al.   FEMS MICROBIOLOGY LETTERS

Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression

(2013) J. M. Taliaferro et al.   GENES & DEVELOPMENT

Multiple roles for Piwi in silencing Drosophila transposons

(2013) N. V. Rozhkov et al.   GENES & DEVELOPMENT

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

(2013) A. Le Thomas et al.   GENES & DEVELOPMENT

CRISPR Regulation of Intraspecies Diversification by Limiting IS Transposition and Intercellular Recombination

(2013) Takayasu Watanabe et al.   Genome Biology and Evolution

Analysis of the transcriptome of Legionella pneumophila hfq mutant reveals a new mobile genetic element

(2013) H. Trigui et al.   MICROBIOLOGY-SGM

An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes

(2013) Xin Zhiguo Li et al.   MOLECULAR CELL

Roles of R2D2, a Cytoplasmic D2 Body Component, in the Endogenous siRNA Pathway in Drosophila

(2013) Kazumichi M. Nishida et al.   MOLECULAR CELL

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

Activation of transposable elements during aging and neuronal decline in Drosophila

(2013) Wanhe Li et al.   NATURE NEUROSCIENCE

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity

(2013) Nicole Darricarrère et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system

(2013) J. A. Ross et al.   RNA

A Conserved Upstream Motif Orchestrates Autonomous, Germline-Enriched Expression of Caenorhabditis elegans piRNAs

(2013) Allison C. Billi et al.   PLoS Genetics

Maternal Depletion of Piwi, a Component of the RNAi System, Impacts Heterochromatin Formation in Drosophila

(2013) Tingting Gu et al.   PLoS Genetics

C. elegans piRNAs Mediate the Genome-wide Surveillance of Germline Transcripts

(2012) Heng-Chi Lee et al.   CELL

Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement

(2012) Wenwen Fang et al.   CELL

Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

(2012) Grzegorz Sienski et al.   CELL

UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery

(2012) Fan Zhang et al.   CELL

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

(2012) Joseph P. Calarco et al.   CELL

piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism

(2012) Ergin Beyret et al.   CELL RESEARCH

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats

(2012) Tzuu-fen Lee et al.   Epigenetics

The Small RNA RteR Inhibits Transfer of the Bacteroides Conjugative Transposon CTnDOT

(2012) J. L. Waters et al.   JOURNAL OF BACTERIOLOGY

Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs

(2012) Germano Cecere et al.   MOLECULAR CELL

In Vitro Transcription Activities of Pol IV, Pol V, and RDR2 Reveal Coupling of Pol IV and RDR2 for dsRNA Synthesis in Plant RNA Silencing

(2012) Jeremy R. Haag et al.   MOLECULAR CELL

The Cochaperone Shutdown Defines a Group of Biogenesis Factors Essential for All piRNA Populations in Drosophila

(2012) Daniel Olivieri et al.   MOLECULAR CELL

Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

RNAi triggered by specialized machinery silences developmental genes and retrotransposons

(2012) Soichiro Yamanaka et al.   NATURE

Structure and function of Zucchini endoribonuclease in piRNA biogenesis

(2012) Hiroshi Nishimasu et al.   NATURE

A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality

(2012) Bethany A. Buckley et al.   NATURE

The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis

(2012) Jonathan J. Ipsaro et al.   NATURE

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

(2012) Xuehua Zhong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA Methylation in Plants: Relationship to Small RNAs and Histone Modifications, and Functions in Transposon Inactivation

(2012) H. Saze et al.   PLANT AND CELL PHYSIOLOGY

Evolutionary Genomics of Transposable Elements in Saccharomyces cerevisiae

(2012) Martin Carr et al.   PLoS One

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

(2012) M. P. Bagijn et al.   SCIENCE

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

(2012) C. A. Ibarra et al.   SCIENCE

Characterization of a piRNA binding protein Miwi in mouse oocytes

(2012) Xiaofang Ding et al.   THERIOGENOLOGY

The tudor domain protein Kumo is required to assemble the nuage and to generate germline piRNAs inDrosophila

(2011) Amit Anand et al.   EMBO JOURNAL

3′ End Formation of PIWI-Interacting RNAs In Vitro

(2011) Shinpei Kawaoka et al.   MOLECULAR CELL

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

(2011) Filippo M. Cernilogar et al.   NATURE

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements

(2011) Serena De Fazio et al.   NATURE

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing

(2011) Michael Reuter 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

MicroRNA Genes Derived from Repetitive Elements and Expanded by Segmental Duplication Events in Mammalian Genomes

(2011) Zhidong Yuan et al.   PLoS One

Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line

(2011) S. H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Protein Complex Required for Polymerase V Transcripts and RNA- Directed DNA Methylation in Arabidopsis

(2010) Julie A. Law et al.   CURRENT BIOLOGY

Repression of Retroelements in Drosophila Germline via piRNA Pathway by the Tudor Domain Protein Tejas

(2010) Veena S. Patil et al.   CURRENT BIOLOGY

An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila

(2010) Daniel Olivieri et al.   EMBO JOURNAL

Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila

(2010) K. Saito et al.   GENES & DEVELOPMENT

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

(2010) C. Biemont   GENETICS

A Domesticated piggyBac Transposase Plays Key Roles in Heterochromatin Dynamics and DNA Cleavage during Programmed DNA Deletion in Tetrahymena thermophila

(2010) Chao-Yin Cheng et al.   MOLECULAR BIOLOGY OF THE CELL

The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Tn10/IS10 transposition is downregulated at the level of transposase expression by the RNA-binding protein Hfq

(2010) Joseph A. Ross et al.   MOLECULAR MICROBIOLOGY

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

(2010) Vianey Olmedo-Monfil et al.   NATURE

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

Repression of transposable-elements – a microRNA anti-cancer defense mechanism?

(2010) Reut Shalgi et al.   TRENDS IN GENETICS

An Effector of RNA-Directed DNA Methylation in Arabidopsis Is an ARGONAUTE 4- and RNA-Binding Protein

(2009) Xin-Jian He et al.   CELL

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary

(2009) Colin D. Malone et al.   CELL

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Marsupial-specific microRNAs evolved from marsupial-specific transposable elements

(2009) Eric J. Devor et al.   GENE

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

Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis

(2009) B. Zheng et al.   GENES & DEVELOPMENT

PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia

(2009) C. Baudry et al.   GENES & DEVELOPMENT

Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line

(2009) N. C. Lau et al.   GENOME RESEARCH

Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline

(2009) Weifeng Gu et al.   MOLECULAR CELL

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Evidence for Co-Evolution between Human MicroRNAs and Alu-Repeats

(2009) Stefan Lehnert et al.   PLoS One

The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila

(2009) Delphine Fagegaltier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAi in Budding Yeast

(2009) I. A. Drinnenberg et al.   SCIENCE

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice

(2009) Alexei A. Aravin et al.   PLoS Genetics

A C. elegans Piwi, PRG-1, Regulates 21U-RNAs during Spermatogenesis

(2008) Guilin Wang et al.   CURRENT BIOLOGY

Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons

(2008) Wei-Jen Chung et al.   CURRENT BIOLOGY

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena

(2008) L. Aronica et al.   GENES & DEVELOPMENT

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline

(2008) Partha P. Das et al.   MOLECULAR CELL

PRG-1 and 21U-RNAs Interact to Form the piRNA Complex Required for Fertility in C. elegans

(2008) Pedro J. Batista et al.   MOLECULAR CELL

Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

(2008) Thomas S. Ream et al.   MOLECULAR CELL

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

(2008) Yoshinori Kawamura et al.   NATURE

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Splicing Factors Facilitate RNAi-Directed Silencing in Fission Yeast

(2008) E. H. Bayne et al.   SCIENCE

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE

Origins and evolution of eukaryotic RNA interference

(2008) S SHABALINA et al.   TRENDS IN ECOLOGY & EVOLUTION