An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans

Nuclear Argonaute Piwi Gene Mutation Affects rRNA by Inducing rRNA Fragment Accumulation, Antisense Expression, and Defective Processing in Drosophila Ovaries

(2020) Anastasia D. Stolyarenko   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants

(2020) Giorgia Barucci et al.   NATURE CELL BIOLOGY

Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons

(2020) Sylvia E. J. Fischer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs in the Transgenerational Inheritance of Epigenetic Information

(2020) Lea Duempelmann et al.   TRENDS IN GENETICS

Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans

(2020) Deniz M. Özata et al.   Nature Ecology & Evolution

HLH-30/TFEB Is a Master Regulator of Reproductive Quiescence

(2020) Birgit Gerisch et al.   DEVELOPMENTAL CELL

poly(UG)-tailed RNAs in genome protection and epigenetic inheritance

(2020) Aditi Shukla et al.   NATURE

Transcription polymerase–catalyzed emergence of novel RNA replicons

(2020) Nimit Jain et al.   SCIENCE

Nucleolar RNA polymerase II drives ribosome biogenesis

(2020) Karan J. Abraham et al.   NATURE

Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans

(2020) Leah Houri-Zeevi et al.   CELL

PIWIL1 promotes gastric cancer via a piRNA-independent mechanism

(2020) Shuo Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Small-RNA-Mediated Feedback Loop Maintains Proper Levels of 22G-RNAs in C. elegans

(2020) Alicia K. Rogers et al.   Cell Reports

Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations

(2019) Lea Duempelmann et al.   MOLECULAR CELL

Assessment and Maintenance of Unigametic Germline Inheritance for C. elegans

(2019) Karen L. Artiles et al.   DEVELOPMENTAL CELL

Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans

(2019) Elif Sarinay Cenik et al.   DEVELOPMENTAL CELL

Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase

(2019) Melanie A. Preston et al.   NATURE METHODS

Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes

(2019) Mitsuhiko P Sato et al.   DNA RESEARCH

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

(2019) Carrie Wright et al.   BMC GENOMICS

Germ Granules Coordinate RNA-Based Epigenetic Inheritance Pathways

(2019) Anne E. Dodson et al.   DEVELOPMENTAL CELL

P Granules Protect RNA Interference Genes from Silencing by piRNAs

(2019) John Paul T. Ouyang et al.   DEVELOPMENTAL CELL

Planarians recruit piRNAs for mRNA turnover in adult stem cells

(2019) Iana V. Kim et al.   GENES & DEVELOPMENT

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion

(2019) Kizhakke Mattada Sathyan et al.   GENES & DEVELOPMENT

Visualization and Quantification of Transposon Activity in Caenorhabditis elegans RNAi Pathway Mutants

(2019) Dylan C. Wallis et al.   G3-Genes Genomes Genetics

FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis

(2019) Chenjiang You et al.   Nature Communications

Challenges and Approaches to Genotyping Repetitive DNA

(2019) Elizabeth A. Morton et al.   G3-Genes Genomes Genetics

A Translation-Activating Function of MIWI/piRNA during Mouse Spermiogenesis

(2019) Peng Dai et al.   CELL

Widespread roles for piRNAs and WAGO-class siRNAs in shaping the germline transcriptome of Caenorhabditis elegans

(2019) Kailee J Reed et al.   NUCLEIC ACIDS RESEARCH

henn-1/HEN1 Promotes Germline Immortality in Caenorhabditis elegans

(2019) Joshua M. Svendsen et al.   Cell Reports

C. elegansADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway

(2018) Daniel P. Reich et al.   GENES & DEVELOPMENT

Mutational and transcriptional landscape of spontaneous gene duplications and deletions inCaenorhabditis elegans

(2018) Anke Konrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes

(2018) Donglei Zhang et al.   SCIENCE

Transgenerational Sterility of Piwi Mutants Represents a Dynamic Form of Adult Reproductive Diapause

(2018) Bree Heestand et al.   Cell Reports

Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation

(2018) Ruby Yu et al.   NATURE

Erroneous ribosomal RNAs promote the generation of antisense ribosomal siRNA

(2018) Chengming Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reactivation of RNA metabolism underlies somatic restoration after adult reproductive diapause in C. elegans

(2018) Nikolay Burnaevskiy et al.   eLife

Unraveling 3′-end RNA uridylation at nucleotide resolution

(2018) Mehdi Pirouz et al.   METHODS

PIWI-interacting RNAs: small RNAs with big functions

(2018) Deniz M. Ozata et al.   NATURE REVIEWS GENETICS

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Caenorhabditis elegans sperm carry a histone-based epigenetic memory of both spermatogenesis and oogenesis

(2018) Tomoko M. Tabuchi et al.   Nature Communications

Chromatin Modifiers SET-25 and SET-32 Are Required for Establishment but Not Long-Term Maintenance of Transgenerational Epigenetic Inheritance

(2018) Rachel M. Woodhouse et al.   Cell Reports

The RNAi Inheritance Machinery of Caenorhabditis elegans

(2017) George Spracklin et al.   GENETICS

RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway

(2017) Xufei Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha

(2017) Jaspreet S. Khurana et al.   RNA

Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans

(2017) Natallia Kalinava et al.   Epigenetics & Chromatin

Tailing and degradation of Argonaute-bound small RNAs protect the genome from uncontrolled RNAi

(2017) Paola Pisacane et al.   Nature Communications

RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway

(2017) Xufei Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNAi Inheritance Machinery of Caenorhabditis elegans

(2017) George Spracklin et al.   GENETICS

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

(2017) Samuel H. Lewis et al.   Nature Ecology & Evolution

A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans

(2016) Leah Houri-Ze’evi et al.   CELL

TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs

(2016) Dmytro Ustianenko et al.   EMBO JOURNAL

Engineered non-Mendelian inheritance of entire parental genomes in C. elegans

(2016) Judith Besseling et al.   NATURE BIOTECHNOLOGY

RNA interference is essential for cellular quiescence

(2016) B. Roche et al.   SCIENCE

A Ribonuclease Coordinates siRNA Amplification and mRNA Cleavage during RNAi

(2015) Hsin-Yue Tsai et al.   CELL

Maternal piRNAs Are Essential for Germline Development following De Novo Establishment of Endo-siRNAs in Caenorhabditis elegans

(2015) Bruno F.M. de Albuquerque et al.   DEVELOPMENTAL CELL

piRNAs and piRNA-Dependent siRNAs Protect Conserved and Essential C. elegans Genes from Misrouting into the RNAi Pathway

(2015) Carolyn M. Phillips et al.   DEVELOPMENTAL CELL

piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis

(2015) Wee Siong Sho Goh et al.   GENES & DEVELOPMENT

Piwi protein as a nucleolus visitor in Drosophila melanogaster

(2015) E. A. Mikhaleva et al.   MOLECULAR BIOLOGY

Regulation of ribosomal DNA amplification by the TOR pathway

(2015) Carmen V. Jack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A deeply conserved, noncanonical miRNA hosted by ribosomal DNA

(2015) Li-Ling Chak et al.   RNA

Genome-wide profiling of theC. elegansdsRNAome

(2015) Joseph M. Whipple et al.   RNA

Polyuridylation in Eukaryotes: A 3′-End Modification Regulating RNA Life

(2015) Paola Munoz-Tello et al.   Biomed Research International

Uridylation by TUT4 and TUT7 Marks mRNA for Degradation

(2014) Jaechul Lim et al.   CELL

Dicer Promotes Transcription Termination at Sites of Replication Stress to Maintain Genome Stability

(2014) Stephane E. Castel et al.   CELL

A Requirement for ERK-Dependent Dicer Phosphorylation in Coordinating Oocyte-to-Embryo Transition in C. elegans

(2014) Melanie Drake et al.   DEVELOPMENTAL CELL

Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice

(2014) J. Castaneda et al.   EMBO JOURNAL

PID-1 is a novel factor that operates during 21U-RNA biogenesis in Caenorhabditis elegans

(2014) B. F. M. de Albuquerque et al.   GENES & DEVELOPMENT

Efficient Marker-Free Recovery of Custom Genetic Modifications with CRISPR/Cas9 in Caenorhabditis elegans

(2014) J. A. Arribere et al.   GENETICS

Determinants of Heterochromatic siRNA Biogenesis and Function

(2014) Ruby Yu et al.   MOLECULAR CELL

Changes in rRNA Transcription Influence Proliferation and Cell Fate Within a Stem Cell Lineage

(2014) Q. Zhang et al.   SCIENCE

Mutation of a Nopp140 gene dao-5 alters rDNA transcription and increases germ cell apoptosis in C. elegans

(2014) C-C Lee et al.   Cell Death & Disease

Reduced Insulin/IGF-1 Signaling Restores Germ Cell Immortality to Caenorhabditis elegans Piwi Mutants

(2014) Matt Simon et al.   Cell Reports

Homologous recombination as a mechanism to recognize repetitive DNA sequences in an RNAi pathway

(2013) Z. Zhang et al.   GENES & DEVELOPMENT

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes

(2013) Z. Shi et al.   GENOME RESEARCH

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

(2013) Xin Zhiguo Li et al.   MOLECULAR CELL

Untangling the web: The diverse functions of the PIWI/piRNA pathway

(2013) Sneha Ramesh Mani et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Intra-Genomic Variation in the Ribosomal Repeats of Nematodes

(2013) Holly M. Bik et al.   PLoS One

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

(2012) Heng-Chi Lee et al.   CELL

piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans

(2012) Alyson Ashe et al.   CELL

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

(2012) Masaki Shirayama et al.   CELL

Protection from Feed-Forward Amplification in an Amplified RNAi Mechanism

(2012) Julia Pak et al.   CELL

Extremely stable Piwi-induced gene silencing inCaenorhabditis elegans

(2012) Maartje J Luteijn et al.   EMBO JOURNAL

A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality

(2012) Bethany A. Buckley et al.   NATURE

Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis

(2012) Anastassios Vourekas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

(2012) M. P. Bagijn et al.   SCIENCE

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity

(2012) Ke Zheng et al.   PLoS Genetics

The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs

(2012) Allison C. Billi et al.   PLoS Genetics

The Influence of Competition Among C. elegans Small RNA Pathways on Development

(2012) Jimmy J. Zhuang et al.   Genes

Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast

(2011) Takehiko Kobayashi   CELLULAR AND MOLECULAR LIFE SCIENCES

EGO-1, a C. elegans RdRP, Modulates Gene Expression via Production of mRNA-Templated Short Antisense RNAs

(2011) Jay M. Maniar et al.   CURRENT BIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Competition between ADAR and RNAi pathways for an extensive class of RNA targets

(2011) Diane Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

(2011) Cameron P. Bracken et al.   NUCLEIC ACIDS RESEARCH

RNA degradome--its biogenesis and functions

(2011) P. Jackowiak et al.   NUCLEIC ACIDS RESEARCH

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

Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns

(2011) Ying Zhang et al.   PLoS Computational Biology

Initiation by a Eukaryotic RNA-dependent RNA Polymerase Requires Looping of the Template End and Is Influenced by the Template-tailing Activity of an Associated Uridyltransferase

(2010) Kristin Benjamin Talsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs

(2010) N. C. Welker et al.   RNA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Quelling targets the rDNA locus and functions in rDNA copy number control

(2009) Germano Cecere et al.   BMC MICROBIOLOGY

The Argonaute CSR-1 and Its 22G-RNA Cofactors Are Required for Holocentric Chromosome Segregation

(2009) Julie M. Claycomb 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

Evolutionarily Conserved Function of RRP36 in Early Cleavages of the Pre-rRNA and Production of the 40S Ribosomal Subunit

(2009) M. Gerus et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2009) Weifeng Gu et al.   MOLECULAR CELL

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

(2009) Heng-Chi Lee et al.   NATURE

High-resolution profiling and discovery of planarian small RNAs

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

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

(2008) Guilin Wang et al.   CURRENT BIOLOGY

Zili is required for germ cell differentiation and meiosis in zebrafish

(2008) Saskia Houwing et al.   EMBO JOURNAL

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

RNA Repair: An Antidote to Cytotoxic Eukaryal RNA Damage

(2008) Jayakrishnan Nandakumar 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

Multimegabase Silencing in Nucleolar Dominance Involves siRNA-Directed DNA Methylation and Specific Methylcytosine-Binding Proteins

(2008) Sasha B. Preuss et al.   MOLECULAR CELL

TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway

(2008) Marc Bühler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The exonuclease ERI-1 has a conserved dual role in 5.8S rRNA processing and RNAi

(2008) Harrison W Gabel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PROMALS3D web server for accurate multiple protein sequence and structure alignments

(2008) J. Pei et al.   NUCLEIC ACIDS RESEARCH

MOLECULAR BIOLOGY: A Tail Tale for U

(2008) M. Wickens et al.   SCIENCE

C. elegans Nucleostemin Is Required for Larval Growth and Germline Stem Cell Division

(2008) Michelle M. Kudron et al.   PLoS Genetics