Acute depletion of the ARID1A subunit of SWI/SNF complexes reveals distinct pathways for activation and repression of transcription

Acute BAF perturbation causes immediate changes in chromatin accessibility

(2021) Sandra Schick et al.   NATURE GENETICS

Mammalian SWI/SNF continuously restores local accessibility to chromatin

(2021) Mario Iurlaro et al.   NATURE GENETICS

Interplay of BAF and MLL4 promotes cell type-specific enhancer activation

(2021) Young-Kwon Park et al.   Nature Communications

mSWI/SNF promotes Polycomb repression both directly and through genome-wide redistribution

(2021) Christopher M. Weber et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of nucleosome-bound human BAF complex

(2020) Shuang He et al.   SCIENCE

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

Mechanisms of OCT4-SOX2 motif readout on nucleosomes

(2020) Alicia K. Michael et al.   SCIENCE

Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex

(2019) Avital Klein-Brill et al.   Cell Reports

Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination

(2019) Josefina Ocampo et al.   GENOME RESEARCH

Profiling of Pluripotency Factors in Single Cells and Early Embryos

(2019) Sarah J. Hainer et al.   CELL

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination

(2019) Lee F Langer et al.   eLife

BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

(2019) William Farnaby et al.   Nature Chemical Biology

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion

(2019) Kizhakke Mattada Sathyan et al.   GENES & DEVELOPMENT

Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

(2019) Sai Li et al.   Cell Reports

ARID1A and PI3-kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion

(2019) Mike R. Wilson et al.   Nature Communications

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

ARID1A and CEBPα cooperatively inhibit UCA1 transcription in breast cancer

(2018) Xiao Guo et al.   ONCOGENE

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

(2018) Nazar Mashtalir et al.   CELL

RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast

(2018) Sandipan Brahma et al.   MOLECULAR CELL

EZH2 variants differentially regulate polycomb repressive complex 2 in histone methylation and cell differentiation

(2018) Weipeng Mu et al.   Epigenetics & Chromatin

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

(2017) Răzvan V. Chereji et al.   MOLECULAR CELL

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

(2017) Greta Pintacuda et al.   MOLECULAR CELL

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

(2017) M Ryan Corces et al.   NATURE METHODS

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers

(2017) Burak H. Alver et al.   Nature Communications

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex

(2017) Payel Sen et al.   Cell Reports

Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers

(2017) Timothy W R Kelso et al.   eLife

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

(2016) Lilien N. Voong et al.   CELL

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

(2016) Maud de Dieuleveult et al.   NATURE

Dynamics of BAF–Polycomb complex opposition on heterochromatin in normal and oncogenic states

(2016) Cigall Kadoch et al.   NATURE GENETICS

SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation

(2016) Xiaofeng Wang et al.   NATURE GENETICS

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice

(2016) Radhika Mathur et al.   NATURE GENETICS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors

(2016) Toyoaki Natsume et al.   Cell Reports

Stepwise nucleosome translocation by RSC remodeling complexes

(2016) Bryan T Harada et al.   eLife

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Coexistent ARID1A–PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signalling

(2015) Ronald L. Chandler et al.   Nature Communications

Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes

(2015) Jesse R. Raab et al.   PLoS Genetics

Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics

(2015) C. Kadoch et al.   Science Advances

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast

(2014) Dwaipayan Ganguli et al.   GENOME RESEARCH

ARID1B is a specific vulnerability in ARID1A-mutant cancers

(2014) Katherine C Helming et al.   NATURE MEDICINE

Transcriptional Repression by the BRG1-SWI/SNF Complex Affects the Pluripotency of Human Embryonic Stem Cells

(2014) Xiaoli Zhang et al.   Stem Cell Reports

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation

(2013) Ulrich M. Zanger et al.   PHARMACOLOGY & THERAPEUTICS

Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters

(2013) M. Y. Tolstorukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Hes1 Desynchronizes Differentiation of Pluripotent Cells by Modulating STAT3 Activity

(2013) Xinzhi Zhou et al.   STEM CELLS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs

(2012) Emily Brookes et al.   Cell Stem Cell

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes

(2012) Matthieu Le Gallo et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3

(2011) Zhe Liu et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

(2011) Lena Ho et al.   NATURE CELL BIOLOGY

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder

(2011) Yaoting Gui et al.   NATURE GENETICS

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer

(2011) Kai Wang et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

ARID1AMutations in Endometriosis-Associated Ovarian Carcinomas

(2010) Kimberly C. Wiegand et al.   NEW ENGLAND JOURNAL OF MEDICINE

Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma

(2010) Siân Jones et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a

(2008) X. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Gene tagging and gene replacement using recombinase-mediated cassette exchange in Schizosaccharomyces pombe

(2007) Adam T. Watson et al.   GENE