The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses

Editorial:Nucleic Acids Researchannual Web Server Issue in 2016

(2016)   NUCLEIC ACIDS RESEARCH

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

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

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

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Standardizing chromatin research: a simple and universal method for ChIP-seq

(2015) Laura Arrigoni et al.   NUCLEIC ACIDS RESEARCH

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

(2015) Vincent J. Lynch et al.   Cell Reports

Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery

(2015) Celeste B. Greer et al.   Cell Reports

piRNAs: from biogenesis to function

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

Role of Tet proteins in enhancer activity and telomere elongation

(2014) Falong Lu et al.   GENES & DEVELOPMENT

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

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

The Histone H3 Lysine 9 Methyltransferases G9a and GLP Regulate Polycomb Repressive Complex 2-Mediated Gene Silencing

(2014) Chiara Mozzetta et al.   MOLECULAR CELL

HSP90α plays an important role in piRNA biogenesis and retrotransposon repression in mouse

(2014) Tomoko Ichiyanagi et al.   NUCLEIC ACIDS RESEARCH

A novel multi-alignment pipeline for high-throughput sequencing data

(2014) S. Huang et al.   Database-The Journal of Biological Databases and Curation

MOF-associated complexes ensure stem cell identity and Xist repression

(2014) Tomasz Chelmicki et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

(2013) Tuncay Baubec et al.   CELL

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish

(2013) N. Rohner et al.   SCIENCE

Transposable elements as genetic regulatory substrates in early development

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

Hsp90@chromatin.nucleus: an emerging hub of a networker

(2013) Ritwick Sawarkar et al.   TRENDS IN CELL BIOLOGY

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

Endogenous retroviruses: acquisition, amplification and taming of genome invaders

(2013) Marie Dewannieux et al.   Current Opinion in Virology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The class I-specific HDAC inhibitor MS-275 modulates the differentiation potential of mouse embryonic stem cells

(2013) G. Franci et al.   Biology Open

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Hsp90 Globally Targets Paused RNA Polymerase to Regulate Gene Expression in Response to Environmental Stimuli

(2012) Ritwick Sawarkar et al.   CELL

Quantitative Analysis of Hsp90-Client Interactions Reveals Principles of Substrate Recognition

(2012) Mikko Taipale et al.   CELL

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

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

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

(2012) Daniel Olivieri et al.   MOLECULAR CELL

A Role for Fkbp6 and the Chaperone Machinery in piRNA Amplification and Transposon Silencing

(2012) Jordi Xiol et al.   MOLECULAR CELL

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A pipeline for the generation of shRNA transgenic mice

(2012) Lukas E Dow et al.   Nature Protocols

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker 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

Retrotransposons: Mobile and mutagenic from conception to death

(2011) Geoffrey J. Faulkner   FEBS LETTERS

KAP1 Protein: An Enigmatic Master Regulator of the Genome

(2011) Sushma Iyengar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90

(2011) Kamalika Moulick et al.   Nature Chemical Biology

Protein Homeostasis and the Phenotypic Manifestation of Genetic Diversity: Principles and Mechanisms

(2010) Daniel F. Jarosz et al.   Annual Review of Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons

(2010) Valeria Specchia et al.   NATURE

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Drosophila Piwi functions in Hsp90-mediated suppression of phenotypic variation

(2010) Vamsi K Gangaraju et al.   NATURE GENETICS

Hsp90 and Environmental Stress Transform the Adaptive Value of Natural Genetic Variation

(2010) D. F. Jarosz et al.   SCIENCE

NVP-AUY922: A Novel Heat Shock Protein 90 Inhibitor Active against Xenograft Tumor Growth, Angiogenesis, and Metastasis

(2008) S. A. Eccles et al.   CANCER RESEARCH

The agouti mouse model: an epigenetic biosensor for nutritional and environmental alterations on the fetal epigenome

(2008) Dana C Dolinoy   NUTRITION REVIEWS

HSP90-buffered genetic variation is common in Arabidopsis thaliana

(2008) T. A. Sangster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY