An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility

Histone H3.3 phosphorylation amplifies stimulation-induced transcription

(2020) Anja Armache et al.   NATURE

SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells

(2019) Parysatis Sachs et al.   Nature Communications

Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency

(2019) Sharon Schlesinger et al.   DEVELOPMENTAL CELL

Phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation

(2019) Sara Martire et al.   NATURE GENETICS

Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing

(2019) Guido A. Stoll et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ZFP57 regulation of transposable elements and gene expression within and beyond imprinted domains

(2019) Hui Shi et al.   Epigenetics & Chromatin

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins

(2019) Simone Sidoli et al.   Scientific Reports

A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells

(2018) Kei Fukuda et al.   GENOME RESEARCH

Structural Basis of Heterochromatin Formation by Human HP1

(2018) Shinichi Machida et al.   MOLECULAR CELL

Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes

(2018) Veronika Ostapcuk et al.   NATURE

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

(2018) Jiangping He et al.   Nature Communications

The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes

(2017) Dong Ding et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

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

(2017) M Ryan Corces et al.   NATURE METHODS

A hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells

(2017) Sharon Schlesinger et al.   NUCLEIC ACIDS RESEARCH

INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers

(2017) Sandipan Brahma et al.   Nature Communications

Structural and mechanistic insights into ATRX-dependent and -independent functions of the histone chaperone DAXX

(2017) Dominik Hoelper et al.   Nature Communications

SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination

(2017) Shu Xiao et al.   Cell Reports

Atrx promotes heterochromatin formation at retrotransposons

(2015) D. Sadic et al.   EMBO REPORTS

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

(2015) Gireesh K. Bogu et al.   MOLECULAR AND CELLULAR BIOLOGY

H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation

(2015) Yoshihiro Matsumura et al.   MOLECULAR CELL

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

(2015) Simon J. Elsässer et al.   NATURE

ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes

(2015) Hsiao P.J. Voon et al.   Cell Reports

Genome-wide analysis of H3.3 dissociation reveals high nucleosome turnover at distal regulatory regions of embryonic stem cells

(2015) Misook Ha et al.   Epigenetics & Chromatin

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

(2014) Li Shen et al.   BMC GENOMICS

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

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

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

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez 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

The ATP-dependent Chromatin Remodeling Enzyme Fun30 Represses Transcription by Sliding Promoter-proximal Nucleosomes

(2013) Boseon Byeon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

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

DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition

(2012) Simon J. Elsässer et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Nucleosome-depleted chromatin gaps recruit assembly factors for the H3.3 histone variant

(2012) J. I. Schneiderman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of Histone H3 Deposition In Vivo Reveal a Nucleosome Gap-Filling Mechanism for H3.3 to Maintain Chromatin Integrity

(2011) Dominique Ray-Gallet et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin

(2011) Sebastian Eustermann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

H3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing

(2011) Irina A Maksakova et al.   Epigenetics & Chromatin

Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

(2011) Srinivas Ramachandran et al.   PLoS Computational Biology

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

(2010) Aaron D. Goldberg et al.   CELL

New functions for an old variant: no substitute for histone H3.3

(2010) Simon J Elsaesser et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

The Snf2 Homolog Fun30 Acts as a Homodimeric ATP-dependent Chromatin-remodeling Enzyme

(2010) Salma Awad et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Nucleosome eviction and activated transcription require p300 acetylation of histone H3 lysine 14

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

Capturing the dynamic epigenome

(2010) Roger B Deal et al.   GENOME BIOLOGY

H2A.Z and H3.3 Histone Variants Affect Nucleosome Structure: Biochemical and Biophysical Studies

(2009) Amit Thakar et al.   BIOCHEMISTRY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Histone chaperones in nucleosome eviction and histone exchange

(2008) Young-Jun Park et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY