Global identification of SWI/SNF targets reveals compensation by EP400

SWI/SNF blockade disrupts PU.1-directed enhancer programs in normal hematopoietic cells and acute myeloid leukemia

(2023) Courtney Chambers et al.   CANCER RESEARCH

Human SMARCA5 is continuously required to maintain nucleosome spacing

(2023) Monica L. Bomber et al.   MOLECULAR CELL

U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes

(2023) Claudia A. Mimoso et al.   MOLECULAR CELL

Targeting SWI/SNF ATPases in H3.3K27M diffuse intrinsic pontine gliomas

(2023) Mateus Mota et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of CRISPR Edits from Sanger Trace Data

(2022) David Conant et al.   CRISPR Journal

Prediction of histone post-translational modification patterns based on nascent transcription data

(2022) Zhong Wang et al.   NATURE GENETICS

Chromatin accessibility profiling by ATAC-seq

(2022) Fiorella C. Grandi et al.   Nature Protocols

Unleashing cell-intrinsic inflammation as a strategy to kill AML blasts

(2022) Jana M. Ellegast et al.   Cancer Discovery

CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming

(2022) Yawei Song et al.   Cell Reports

Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential

(2022) Hanneke Vlaming et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss of TIP60 (KAT5) abolishes H2AZ lysine 7 acetylation and causes p53, INK4A, and ARF-independent cell cycle arrest

(2022) Johannes Wichmann et al.   Cell Death & Disease

Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci

(2022) Chad B. Stein et al.   MOLECULAR CELL

Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation

(2022) Justyna A. Janas et al.   MOLECULAR CELL

Transcription shapes genome-wide histone acetylation patterns

(2021) Benjamin J. E. Martin et al.   Nature Communications

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

Integrated cross-study datasets of genetic dependencies in cancer

(2021) Clare Pacini et al.   Nature Communications

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

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

Metformin Reduces Histone H3K4me3 at the Promoter Regions of Positive Cell Cycle Regulatory Genes in Lung Cancer Cells

(2021) Dongho Kim et al.   Cancers

Intrinsically disordered Meningioma-1 stabilizes the BAF complex to cause AML

(2021) Simone S. Riedel et al.   MOLECULAR CELL

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

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

In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin

(2021) Ben C Tilly et al.   eLife

Exquisite Sensitivity to Dual BRG1/BRM ATPase Inhibitors Reveals Broad SWI/SNF Dependencies in Acute Myeloid Leukemia

(2021) Florencia Rago et al.   MOLECULAR CANCER RESEARCH

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

(2021) Seraina Blümli et al.   Cell Reports

Darolutamide antagonizes androgen signaling by blocking enhancer and super‐enhancer activation

(2020) Simon J. Baumgart et al.   Molecular Oncology

A WIZ/Cohesin/CTCF Complex Anchors DNA Loops to Define Gene Expression and Cell Identity

(2020) Megan Justice et al.   Cell Reports

Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes

(2020) Andrea Halaburkova et al.   GENOME RESEARCH

Transcription imparts architecture, function and logic to enhancer units

(2020) Nathaniel D. Tippens et al.   NATURE GENETICS

Mammalian SWI/SNF Chromatin Remodeling Complexes: Emerging Mechanisms and Therapeutic Strategies

(2020) Richard C. Centore et al.   TRENDS IN GENETICS

Identification of AR-V7 downstream genes commonly targeted by AR/AR-V7 and specifically targeted by AR-V7 in castration resistant prostate cancer

(2020) Masahiro Sugiura et al.   Translational Oncology

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

(2019) Swetansu K. Hota et al.   DEVELOPMENT

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

(2019) Darko Barisic et al.   NATURE

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

(2018) Mariella G. Filbin et al.   SCIENCE

Identification of regulatory elements from nascent transcription using dREG

(2018) Zhong Wang et al.   GENOME RESEARCH

Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers

(2018) Julien P. N. Papillon et al.   JOURNAL OF MEDICINAL CHEMISTRY

Transcription control by the ENL YEATS domain in acute leukaemia

(2017) Michael A. Erb et al.   NATURE

SMARCB1 is required for widespread BAF complex–mediated activation of enhancers and bivalent promoters

(2017) Robert T Nakayama et al.   NATURE GENETICS

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

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

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

Novel synthetic lethality screening method identifies TIP60-dependent radiation sensitivity in the absence of BAF180

(2016) Suzanna R. Hopkins et al.   DNA REPAIR

Mechanism of Histone H3K4me3 Recognition by the Plant Homeodomain of Inhibitor of Growth 3

(2016) Sophia Kim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2016) Maud de Dieuleveult et al.   NATURE

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

7SK-BAF axis controls pervasive transcription at enhancers

(2016) Ryan A Flynn et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

H2A.Z acetylation and transcription: ready, steady, go!

(2016) Yolanda Colino-Sanguino et al.   Epigenomics

7SK-BAF axis controls pervasive transcription at enhancers

(2016) Ryan A Flynn et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

(2016) Nicola Wiechens et al.   PLoS Genetics

The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies

(2015) Bhavatarini Vangamudi et al.   CANCER RESEARCH

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

(2015) Sarah J. Hainer et al.   GENES & DEVELOPMENT

Expression of Non-acetylatable H2A.Z in Myoblast Cells Blocks Myoblast Differentiation through Disruption of MyoD Expression

(2015) Cindy Law et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The chromatin remodeler Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth

(2015) Claudia Bossen et al.   NATURE IMMUNOLOGY

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells

(2015) Sarina Ravens et al.   Epigenetics & Chromatin

Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives

(2014) Blaine Bartholomew   Annual Review of Biochemistry

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines

(2014) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Xiaoli Zhang et al.   Stem Cell Reports

A Synthetic Lethality-Based Strategy to Treat Cancers Harboring a Genetic Deficiency in the Chromatin Remodeling Factor BRG1

(2013) T. Oike et al.   CANCER RESEARCH

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

(2013) Cigall Kadoch et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Chromatin regulation Tip(60)s the balance in embryonic stem cell self-renewal

(2010) Thomas G. Fazzio et al.   CELL CYCLE

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Roles for H2A.Z and Its Acetylation in GAL1 Transcription and Gene Induction, but Not GAL1-Transcriptional Memory

(2010) Jeffrey E. Halley et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity

(2008) Thomas G. Fazzio et al.   CELL

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics