Evidence of pioneer factor activity of an oncogenic fusion transcription factor

St. Jude Cloud-a Pediatric Cancer Genomic Data Sharing Ecosystem

(2021) Clay McLeod et al.   Cancer Discovery

Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP)

(2020) Berkley E. Gryder et al.   Nature Protocols

Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin

(2020) Jonathan Lerner et al.   MOLECULAR CELL

Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

(2020) Ezequiel Miron et al.   Science Advances

Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms

(2020) Bing-Rui Zhou et al.   MOLECULAR CELL

Forkhead Transcription Factors in Health and Disease

(2020) Laetitia Herman et al.   TRENDS IN GENETICS

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine

(2019) Jie Yang et al.   NUCLEIC ACIDS RESEARCH

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

(2019) Benjamin T Donovan et al.   eLife

OLIG2 is a marker of the fusion protein-driven neurodevelopmental transcriptional signature in alveolar rhabdomyosarcoma

(2019) Shyam S. Raghavan et al.   HUMAN PATHOLOGY

Structural Features of Transcription Factors Associating with Nucleosome Binding

(2019) Meilin Fernandez Garcia et al.   MOLECULAR CELL

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

(2019) Berkley E. Gryder et al.   NATURE GENETICS

Systematic Study of Nucleosome-Displacing Factors in Budding Yeast

(2018) Chao Yan et al.   MOLECULAR CELL

MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma

(2018) Marielle E. Yohe et al.   Science Translational Medicine

A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes

(2018) Sheila S Teves et al.   eLife

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

PAX3-FOXO1 is essential for tumour initiation and maintenance but not recurrence in a human myoblast model of rhabdomyosarcoma

(2017) Puspa R Pandey et al.   JOURNAL OF PATHOLOGY

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes

(2017) Justin S. Becker et al.   MOLECULAR CELL

PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability

(2017) Berkley E. Gryder et al.   Cancer Discovery

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

(2016) Cédric Deluz et al.   GENES & DEVELOPMENT

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin

(2016) Benjamin Z Stanton et al.   NATURE GENETICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition

(2016) Brian Egan et al.   PLoS One

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Loading of PAX3 to Mitotic Chromosomes Is Mediated by Arginine Methylation and Associated with Waardenburg Syndrome

(2015) Tsu-Fang Wu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Clonality and Evolutionary History of Rhabdomyosarcoma

(2015) Li Chen et al.   PLoS Genetics

Histone H4 Lys 20 Monomethylation of the CENP-A Nucleosome Is Essential for Kinetochore Assembly

(2014) Tetsuya Hori et al.   DEVELOPMENTAL CELL

Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

(2014) J. F. Shern et al.   Cancer Discovery

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

Reversible Disruption of mSWI/SNF (BAF) Complexes by the SS18-SSX Oncogenic Fusion in Synovial Sarcoma

(2013) Cigall Kadoch et al.   CELL

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

(2013) Warren A. Whyte et al.   CELL

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

Epigenetic Reprogramming in Cancer

(2013) M. L. Suva et al.   SCIENCE

The Pediatric Cancer Genome Project

(2012) James R Downing et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A transcription factor–based mechanism for mouse heterochromatin formation

(2012) Aydan Bulut-Karslioglu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Pioneer transcription factors: establishing competence for gene expression

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

Genome-Wide Identification of PAX3-FKHR Binding Sites in Rhabdomyosarcoma Reveals Candidate Target Genes Important for Development and Cancer

(2010) L. Cao et al.   CANCER RESEARCH

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

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Structural Basis for DNA Recognition by the Human PAX3 Homeodomain†,‡

(2009) Gabriel Birrane et al.   BIOCHEMISTRY

Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene

(2009) Shyra J. Miller et al.   EMBO Molecular Medicine

Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification

(2008) Michael M. Brent et al.   STRUCTURE