Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets

(2014) Kavitha Sarma et al.   CELL

Histone H3.3 Is Required to Maintain Replication Fork Progression after UV Damage

(2014) Alexander Frey et al.   CURRENT BIOLOGY

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

(2014) Aydan Bulut-Karslioglu et al.   MOLECULAR CELL

DAXX co-folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues

(2014) Jamie E. DeNizio et al.   NUCLEIC ACIDS RESEARCH

A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters

(2014) Ozlem Yildirim et al.   PLoS Genetics

Hira-Dependent Histone H3.3 Deposition Facilitates PRC2 Recruitment at Developmental Loci in ES Cells

(2013) Laura A. Banaszynski et al.   CELL

Transcription Recovery after DNA Damage Requires Chromatin Priming by the H3.3 Histone Chaperone HIRA

(2013) Salomé Adam et al.   CELL

H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin

(2013) P. Chen et al.   GENES & DEVELOPMENT

Distinct and Combinatorial Functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in Mouse Embryonic Stem Cell Identity

(2013) Partha Pratim Das et al.   MOLECULAR CELL

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells

(2012) H. M. Rowe et al.   GENOME RESEARCH

Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations

(2012) C. Robberecht et al.   GENOME RESEARCH

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Endogenous viruses: insights into viral evolution and impact on host biology

(2012) Cédric Feschotte et al.   NATURE REVIEWS GENETICS

Epigenetic interplay between mouse endogenous retroviruses and host genes

(2012) Rita Rebollo et al.   GENOME BIOLOGY

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

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3

(2010) P. Drane et al.   GENES & DEVELOPMENT

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres

(2010) P. W. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

(2009) Mark S Longo et al.   BMC GENOMICS

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

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

Histone H3.3 incorporation provides a unique and functionally essential telomeric chromatin in embryonic stem cells

(2009) L. H. Wong et al.   GENOME RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Endogenous retroviruses

(2008) I. A. Maksakova et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

An infectious progenitor for the murine IAP retrotransposon: Emergence of an intracellular genetic parasite from an ancient retrovirus

(2008) D. Ribet et al.   GENOME RESEARCH

Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

(2008) Jungnam Lee et al.   PLoS One

Genome-Wide Assessments Reveal Extremely High Levels of Polymorphism of Two Active Families of Mouse Endogenous Retroviral Elements

(2008) Ying Zhang et al.   PLoS Genetics