A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress

Buried territories: heterochromatic response to DNA double-strand breaks

(2016) Yi-Li Feng et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

LINE-1 silencing by retinoblastoma proteins is effected through the nucleosomal and remodeling deacetylase multiprotein complex

(2016) Diego E. Montoya-Durango et al.   BMC CANCER

Direct interrogation of the role of H3K9 in metazoan heterochromatin function

(2016) Taylor J.R. Penke et al.   GENES & DEVELOPMENT

Patching Broken DNA: Nucleosome Dynamics and the Repair of DNA Breaks

(2016) Ozge Gursoy-Yuzugullu et al.   JOURNAL OF MOLECULAR BIOLOGY

Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability

(2016) Peter Zeller et al.   NATURE GENETICS

New Insights into the Regulation of Heterochromatin

(2016) Jiyong Wang et al.   TRENDS IN GENETICS

The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic

(2016) Joel M Swenson et al.   eLife

PIWI-Interacting RNA: Its Biogenesis and Functions

(2015) Yuka W. Iwasaki et al.   Annual Review of Biochemistry

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

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

(2015) Hui Mao et al.   CURRENT BIOLOGY

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

The DREAM complex promotes gene body H2A.Z for target repression

(2015) Isabel Latorre et al.   GENES & DEVELOPMENT

RNA-mediated epigenetic regulation of gene expression

(2015) Daniel Holoch et al.   NATURE REVIEWS GENETICS

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

SETDB1, HP1 and SUV39 promote repositioning of 53BP1 to extend resection during homologous recombination in G2 cells

(2015) Meryem Alagoz et al.   NUCLEIC ACIDS RESEARCH

RNAi and Heterochromatin Assembly

(2015) Robert Martienssen et al.   Cold Spring Harbor Perspectives in Biology

Constitutive heterochromatin formation and transcription in mammals

(2015) Nehmé Saksouk et al.   Epigenetics & Chromatin

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

piRNAs: from biogenesis to function

(2014) E.-M. Weick et al.   DEVELOPMENT

Chromatin regulation: How complex does it get?

(2014) Karin Meier et al.   Epigenetics

Setdb1is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

(2014) Sheng Liu et al.   GENES & DEVELOPMENT

Defining heterochromatin inC. elegansthrough genome-wide analysis of the heterochromatin protein 1 homolog HPL-2

(2014) Jacob M. Garrigues et al.   GENOME RESEARCH

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

C. elegans CEP-1/p53 and BEC-1 Are Involved in DNA Repair

(2014) Sandy Hoffman et al.   PLoS One

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

Differential contribution of HP1 proteins to DNA end resection and homology-directed repair

(2013) Gaston Soria et al.   CELL CYCLE

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

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

HPV 5 and 8 E6 expression reduces ATM protein levels and attenuates LINE-1 retrotransposition

(2013) Nicholas A. Wallace et al.   VIROLOGY

Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells

(2013) Irina A Maksakova et al.   Epigenetics & Chromatin

A Role for the Malignant Brain Tumour (MBT) Domain Protein LIN-61 in DNA Double-Strand Break Repair by Homologous Recombination

(2013) Nicholas M. Johnson et al.   PLoS 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

Step-Wise Methylation of Histone H3K9 Positions Heterochromatin at the Nuclear Periphery

(2012) Benjamin D. Towbin et al.   CELL

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

(2012) Masaki Shirayama et al.   CELL

NuRD and Pluripotency: A Complex Balancing Act

(2012) Guang Hu et al.   Cell Stem Cell

Extremely stable Piwi-induced gene silencing inCaenorhabditis elegans

(2012) Maartje J Luteijn et al.   EMBO JOURNAL

Chromodomain Helicase DNA-binding Protein 4 (CHD4) Regulates Homologous Recombination DNA Repair, and Its Deficiency Sensitizes Cells to Poly(ADP-ribose) Polymerase (PARP) Inhibitor Treatment

(2012) Mei-Ren Pan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Heterochromatin protein 1 homologue Swi6 acts in concert with Ers1 to regulate RNAi-directed heterochromatin assembly

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

Ers1 links HP1 to RNAi

(2012) M. Rougemaille et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repression of Germline RNAi Pathways in Somatic Cells by Retinoblastoma Pathway Chromatin Complexes

(2012) Xiaoyun Wu et al.   PLoS Genetics

Transcriptional Repression of Hox Genes by C. elegans HP1/HPL and H1/HIS-24

(2012) Maja Studencka et al.   PLoS Genetics

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

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

(2011) Irene Chiolo et al.   CELL

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

synMuv B proteins antagonize germline fate in the intestine and ensure C. elegans survival

(2011) L. N. Petrella et al.   DEVELOPMENT

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans

(2011) N. O. Burton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

H3K9me2/3 Binding of the MBT Domain Protein LIN-61 Is Essential for Caenorhabditis elegans Vulva Development

(2011) Nora Koester-Eiserfunke et al.   PLoS Genetics

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

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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans

(2010) Ky Sha et al.   BMC GENOMICS

Gene Silencing: Small RNAs Control RNA Polymerase II Elongation

(2010) Mariano Alló et al.   CURRENT BIOLOGY

Regulation of DNA-damage responses and cell-cycle progression by the chromatin remodelling factor CHD4

(2010) Sophie E Polo et al.   EMBO JOURNAL

HP1: Heterochromatin binding proteins working the genome

(2010) Weihua Zeng et al.   Epigenetics

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

The NuRD chromatin–remodeling complex regulates signaling and repair of DNA damage

(2010) Godelieve Smeenk et al.   JOURNAL OF CELL BIOLOGY

The chromatin-remodeling factor CHD4 coordinates signaling and repair after DNA damage

(2010) Dorthe Helena Larsen et al.   JOURNAL OF CELL BIOLOGY

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

(2010) Shouhong Guang et al.   NATURE

Different Mi-2 Complexes for Various Developmental Functions in Caenorhabditis elegans

(2010) Myriam Passannante et al.   PLoS One

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

(2010) Kohta Ikegami et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Recombinational Repair within Heterochromatin Requires ATP-Dependent Chromatin Remodeling

(2009) Manisha Sinha et al.   CELL

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells

(2009) P. Yuan et al.   GENES & DEVELOPMENT

Heterochromatin protein 1 is recruited to various types of DNA damage

(2009) Martijn S. Luijsterburg et al.   JOURNAL OF CELL BIOLOGY

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

(2009) Weifeng Gu et al.   MOLECULAR CELL

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

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

(2008) Guilin Wang et al.   CURRENT BIOLOGY

Caenorhabditis elegans POLQ-1 and HEL-308 function in two distinct DNA interstrand cross-link repair pathways

(2008) Diego M. Muzzini et al.   DNA REPAIR

HP1 Proteins Form Distinct Complexes and Mediate Heterochromatic Gene Silencing by Nonoverlapping Mechanisms

(2008) Mohammad R. Motamedi 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

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

An Argonaute Transports siRNAs from the Cytoplasm to the Nucleus

(2008) S. Guang et al.   SCIENCE