RNAi pathways repress reprogramming of C. elegans germ cells during heat stress

Sperm-inherited H3K27me3 impacts offspring transcription and development in C. elegans

(2019) Kiyomi Raye Kaneshiro et al.   Nature Communications

H3K9me3 is required for inheritance of small RNAs that target a unique subset of newly evolved genes

(2019) Itamar Lev et al.   eLife

Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

(2019) Mei Han et al.   BMC GENOMICS

The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation

(2019) Maria Ninova et al.   MOLECULAR CELL

Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing

(2019) Maria Ninova et al.   MOLECULAR 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

Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of Mutator foci

(2018) Celja J. Uebel et al.   PLoS Genetics

NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors

(2018) John M. Gaspar   BMC BIOINFORMATICS

The H3K9 methyltransferase SETDB1 maintains female identity in Drosophila germ cells

(2018) Anne E. Smolko et al.   Nature Communications

C. elegans Heterochromatin Factor SET-32 Plays an Essential Role in Transgenerational Establishment of Nuclear RNAi-Mediated Epigenetic Silencing

(2018) Natallia Kalinava et al.   Cell Reports

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

Germ Granules Prevent Accumulation of Somatic Transcripts in the AdultCaenorhabditis elegansGermline

(2017) Andrew Kekūpa’a Knutson et al.   GENETICS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

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

The RNAi Inheritance Machinery of Caenorhabditis elegans

(2017) George Spracklin et al.   GENETICS

Germ Granules Prevent Accumulation of Somatic Transcripts in the AdultCaenorhabditis elegansGermline

(2017) Andrew Kekūpa’a Knutson et al.   GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans

(2016) Julie Zhouli Ni et al.   Epigenetics & Chromatin

Increasing Notch signaling antagonizes PRC2-mediated silencing to promote reprograming of germ cells into neurons

(2016) Stefanie Seelk et al.   eLife

WormExp: a web-based application for aCaenorhabditis elegans-specific gene expression enrichment analysis

(2015) Wentao Yang et al.   BIOINFORMATICS

A Ribonuclease Coordinates siRNA Amplification and mRNA Cleavage during RNAi

(2015) Hsin-Yue Tsai et al.   CELL

The Nrde Pathway Mediates Small-RNA-Directed Histone H3 Lysine 27 Trimethylation in Caenorhabditis elegans

(2015) Hui Mao et al.   CURRENT BIOLOGY

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

(2015) A. C. Campbell et al.   DEVELOPMENT

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

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Enrichment of H3K9me2 on Unsynapsed Chromatin in Caenorhabditis elegans Does Not Target de Novo Sites

(2015) Yiqing Guo et al.   G3-Genes Genomes Genetics

Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans

(2015) Julie Ni et al.   BMC GENOMICS

Ancient Endo-siRNA Pathways Reveal New Tricks

(2014) Julie M. Claycomb   CURRENT BIOLOGY

Germ-Granule Components Prevent Somatic Development in the C. elegans Germline

(2014) Dustin L. Updike et al.   CURRENT BIOLOGY

MUT-14 and SMUT-1 DEAD Box RNA Helicases Have Overlapping Roles in Germline RNAi and Endogenous siRNA Formation

(2014) Carolyn M. Phillips et al.   CURRENT BIOLOGY

SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line

(2014) Shana C. Kerr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Caenorhabditis elegans RSD-2 and RSD-6 promote germ cell immortality by maintaining small interfering RNA populations

(2014) A. Sakaguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The SET-2/SET1 Histone H3K4 Methyltransferase Maintains Pluripotency in the Caenorhabditis elegans Germline

(2014) Valérie J. Robert et al.   Cell Reports

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

(2014) Matt Simon et al.   Cell Reports

A Histone Methylation Network Regulates Transgenerational Epigenetic Memory in C. elegans

(2014) Eric L. Greer et al.   Cell Reports

LET-418/Mi2 and SPR-5/LSD1 Cooperatively Prevent Somatic Reprogramming of C. elegans Germline Stem Cells

(2014) Stéphanie Käser-Pébernard et al.   Stem Cell Reports

H3K4 demethylase activities repress proliferative and postmitotic aging

(2013) Stacy M. Alvares et al.   AGING CELL

Argonautes Promote Male Fertility and Provide a Paternal Memory of Germline Gene Expression in C. elegans

(2013) Colin C. Conine et al.   CELL

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

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

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

MUT-16 promotes formation of perinuclear Mutator foci required for RNA silencing in the C. elegans germline

(2012) C. M. Phillips et al.   GENES & DEVELOPMENT

Germ granules and the control of mRNA translation

(2012) Madhu S. Sengupta et al.   IUBMB LIFE

A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality

(2012) Bethany A. Buckley et al.   NATURE

Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

(2012) Sam Guoping Gu et al.   NATURE GENETICS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Removal of Polycomb Repressive Complex 2 Makes C. elegans Germ Cells Susceptible to Direct Conversion into Specific Somatic Cell Types

(2012) Tulsi Patel et al.   Cell Reports

PIWI Associated siRNAs and piRNAs Specifically Require the Caenorhabditis elegans HEN1 Ortholog henn-1

(2012) Taiowa A. Montgomery et al.   PLoS Genetics

The Many Faces of RNAi

(2011) René F. Ketting   DEVELOPMENTAL CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

mut-16 and other mutator class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans

(2011) C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Caenorhabditis elegans chromatin-associated proteins SET-2 and ASH-2 are differentially required for histone H3 Lys 4 methylation in embryos and adult germ cells

(2011) Y. Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

(2011) Sylvia E. J. Fischer et al.   PLoS Genetics

A Pre-mRNA–Associating Factor Links Endogenous siRNAs to Chromatin Regulation

(2011) Kirk B. Burkhart et al.   PLoS Genetics

A Role for Set1/MLL-Related Components in Epigenetic Regulation of the Caenorhabditis elegans Germ Line

(2011) Tengguo Li et al.   PLoS Genetics

Distinct Phases of siRNA Synthesis in an Endogenous RNAi Pathway in C. elegans Soma

(2010) Jonathan I. Gent et al.   MOLECULAR CELL

Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription

(2010) Shouhong Guang et al.   NATURE

Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway

(2010) Jessica J. Vasale et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Conversion of C. elegans Germ Cells into Specific Neuron Types

(2010) B. Tursun et al.   SCIENCE

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

(2009) Julie M. Claycomb et al.   CELL

A C. elegans LSD1 Demethylase Contributes to Germline Immortality by Reprogramming Epigenetic Memory

(2009) David J. Katz et al.   CELL

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

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

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

(2009) Weifeng Gu et al.   MOLECULAR CELL

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system

(2008) Joseph D Watson et al.   BMC GENOMICS

An Argonaute Transports siRNAs from the Cytoplasm to the Nucleus

(2008) S. Guang et al.   SCIENCE

Argonaute proteins: key players in RNA silencing

(2007) Gyorgy Hutvagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY