STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution

(2020) Marie-Ming Aynaud et al.   Cell Reports

Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control

(2020) Valentina Casa et al.   GENOME RESEARCH

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Combined Cohesin–RUNX1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes

(2020) Yotaro Ochi et al.   Cancer Discovery

Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells

(2020) Nicole L. Arruda et al.   Epigenetics & Chromatin

Essential Roles of Cohesin STAG2 in Mouse Embryonic Development and Adult Tissue Homeostasis

(2020) Magali De Koninck et al.   Cell Reports

Chronic loss of STAG2 leads to altered chromatin structure contributing to de-regulated transcription in AML

(2020) James S. Smith et al.   Journal of Translational Medicine

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation

(2019) Aaron D. Viny et al.   Cell Stem Cell

Fundamental roles of chromatin loop extrusion in antibody class switching

(2019) Xuefei Zhang et al.   NATURE

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Hippo pathway effectors YAP1/TAZ induce an EWS–FLI1 ‐opposing gene signature and associate with disease progression in Ewing sarcoma

(2019) Pablo Rodríguez‐Núñez et al.   JOURNAL OF PATHOLOGY

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in cancer

(2018) Yunhua Liu et al.   JOURNAL OF CLINICAL INVESTIGATION

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

(2018) Aleksandar Kojic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

(2018) Aleksandar Kojic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ewing sarcoma

(2018) Thomas G. P. Grünewald et al.   Nature Reviews Disease Primers

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Epigenome editing of microsatellite repeats defines tumor-specific enhancer functions and dependencies

(2018) Gaylor Boulay et al.   GENES & DEVELOPMENT

Towards a Unified Model of SMC Complex Function

(2018) Markus Hassler et al.   CURRENT BIOLOGY

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

(2017) Nathan C Sheffield et al.   NATURE MEDICINE

Cell-to-cell heterogeneity of EWSR1-FLI1 activity determines proliferation/migration choices in Ewing sarcoma cells

(2017) G-A Franzetti et al.   ONCOGENE

EWS-FLI1 perturbs MRTFB/YAP-1/TEAD target gene regulation inhibiting cytoskeletal autoregulatory feedback in Ewing sarcoma

(2017) A M Katschnig et al.   ONCOGENE

Synthetic lethal interaction between the tumour suppressor STAG2 and its paralog STAG1

(2017) Lorena Benedetti et al.   Oncotarget

Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets

(2017) Michaela C. Baldauf et al.   Oncotarget

Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts

(2017) Petra van der Lelij et al.   eLife

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

Activation of Wnt/ -Catenin in Ewing Sarcoma Cells Antagonizes EWS/ETS Function and Promotes Phenotypic Transition to More Metastatic Cell States

(2016) E. A. Pedersen et al.   CANCER RESEARCH

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Functional, chemical genomic, and super-enhancer screening identify sensitivity to cyclin D1/CDK4 pathway inhibition in Ewing sarcoma

(2015) Alyssa L. Kennedy et al.   Oncotarget

Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1

(2015) Eleni M. Tomazou et al.   Cell Reports

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

(2014) Nicolò Riggi et al.   CANCER CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

The Genomic Landscape of Pediatric Ewing Sarcoma

(2014) B. D. Crompton et al.   Cancer Discovery

Genomic Landscape of Ewing Sarcoma Defines an Aggressive Subtype with Co-Association of STAG2 and TP53 Mutations

(2014) F. Tirode et al.   Cancer Discovery

The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation

(2014) Andrew S. Brohl et al.   PLoS Genetics

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

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Characterization of the Interaction between the Cohesin Subunits Rad21 and SA1/2

(2013) Nenggang Zhang et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Targeting the EWSR1-FLI1 Oncogene-Induced Protein Kinase PKC-  Abolishes Ewing Sarcoma Growth

(2012) D. Surdez et al.   CANCER RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Common variants near TARDBP and EGR2 are associated with susceptibility to Ewing sarcoma

(2012) Sophie Postel-Vinay et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Specific Sites in the C Terminus of CTCF Interact with the SA2 Subunit of the Cohesin Complex and Are Required for Cohesin-Dependent Insulation Activity

(2011) T. Xiao et al.   MOLECULAR AND CELLULAR BIOLOGY

Mutational Inactivation of STAG2 Causes Aneuploidy in Human Cancer

(2011) D. A. Solomon et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

EWS/ETS Regulates the Expression of the Dickkopf Family in Ewing Family Tumor Cells

(2009) Yoshitaka Miyagawa et al.   PLoS One

The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function

(2009) Noëlle Guillon et al.   PLoS One

A Molecular Function Map of Ewing's Sarcoma

(2009) Maximilian Kauer et al.   PLoS One

EWS-FLI-1 Expression Triggers a Ewing's Sarcoma Initiation Program in Primary Human Mesenchymal Stem Cells

(2008) N. Riggi et al.   CANCER RESEARCH

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Microsatellites as EWS/FLI response elements in Ewing's sarcoma

(2008) K. Gangwal 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