Transcription-mediated supercoiling regulates genome folding and loop formation

Transcription organizes euchromatin via microphase separation

(2021) Lennart Hilbert et al.   Nature Communications

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

Visualizing the genome in high resolution challenges our textbook understanding

(2020) Melike Lakadamyali et al.   NATURE METHODS

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Landscape of cohesin-mediated chromatin loops in the human genome

(2020) Fabian Grubert et al.   NATURE

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

(2020) Huy Q. Nguyen et al.   NATURE METHODS

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization

(2019) M. Jordan Rowley et al.   Cell Reports

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

(2019) Andrés M. Cardozo Gizzi et al.   MOLECULAR CELL

Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II

(2019) Ryosuke Nagashima et al.   JOURNAL OF CELL BIOLOGY

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology

(2019) Enzo Orlandini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations

(2019) Henrike Johanna Gothe et al.   MOLECULAR CELL

Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity

(2019) Andres Canela et al.   MOLECULAR CELL

Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA

(2019) Antonio Valdés et al.   NUCLEIC ACIDS RESEARCH

Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo

(2019) Jason Otterstrom et al.   NUCLEIC ACIDS RESEARCH

Differential contribution of steady‐state RNA and active transcription in chromatin organization

(2019) A Rasim Barutcu et al.   EMBO REPORTS

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

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

OUP accepted manuscript

(2018)   BIOINFORMATICS

DNA Supercoiling, Topoisomerases, and Cohesin: Partners in Regulating Chromatin Architecture?

(2018) Camilla Björkegren et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Protein-mediated loops in supercoiled DNA create large topological domains

(2018) Yan Yan et al.   NUCLEIC ACIDS RESEARCH

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

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

Are TADs supercoiled?

(2018) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Bogdan Bintu et al.   SCIENCE

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

TrackMate: An open and extensible platform for single-particle tracking

(2017) Jean-Yves Tinevez et al.   METHODS

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger et al.   NATURE

A DNA origami platform for quantifying protein copy number in super-resolution

(2017) Francesca Cella Zanacchi et al.   NATURE METHODS

Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes

(2017) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

DNA knots occur in intracellular chromatin

(2017) Antonio Valdés et al.   NUCLEIC ACIDS RESEARCH

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

(2017) Xindan Wang et al.   SCIENCE

SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription

(2017) Ngat T. Tran et al.   Cell Reports

Cohesin Can Remain Associated with Chromosomes during DNA Replication

(2017) James D.P. Rhodes et al.   Cell Reports

Scc2/Nipbl hops between chromosomal cohesin rings after loading

(2017) James Rhodes et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

Rapid movement and transcriptional re‐localization of human cohesin on DNA

(2016) Iain F Davidson et al.   EMBO JOURNAL

EPOP Functionally Links Elongin and Polycomb in Pluripotent Stem Cells

(2016) Malte Beringer et al.   MOLECULAR CELL

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Roles of eukaryotic topoisomerases in transcription, replication and genomic stability

(2016) Yves Pommier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single molecule tracking of Ace1p inSaccharomyces cerevisiaedefines a characteristic residence time for non-specific interactions of transcription factors with chromatin

(2016) David A. Ball et al.   NUCLEIC ACIDS RESEARCH

ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy

(2016) Leonid Andronov et al.   Scientific Reports

On characterizing protein spatial clusters with correlation approaches

(2016) Arun Shivanandan et al.   Scientific Reports

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

(2016) Johannes Stigler et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Evidence for cohesin sliding along budding yeast chromosomes

(2016) Maria Ocampo-Hafalla et al.   Open Biology

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the β-globin locus

(2015) Yea Woon Kim et al.   BIOSCIENCE REPORTS

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data

(2015) Florian Levet et al.   NATURE METHODS

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

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Constitutive heterochromatin formation and transcription in mammals

(2015) Nehmé Saksouk et al.   Epigenetics & Chromatin

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils

(2014) X. Fernandez et al.   EMBO JOURNAL

TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO–IKK supramolecular structures

(2014) Nadine Tarantino et al.   JOURNAL OF CELL BIOLOGY

A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS

(2014) Jessica Zuin et al.   PLoS Genetics

Supercoiling in DNA and chromatin

(2013) Nick Gilbert et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Wapl is an essential regulator of chromatin structure and chromosome segregation

(2013) Antonio Tedeschi et al.   NATURE

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

FSHD muscular dystrophy region gene 1 binds Suv4-20h1 histone methyltransferase and impairs myogenesis

(2013) Maria Victoria Neguembor et al.   Journal of Molecular Cell Biology

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

Topoisomerase II is required for the production of long Pol II gene transcripts in yeast

(2012) Ricky S. Joshi et al.   NUCLEIC ACIDS RESEARCH

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

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

DNA Topoisomerases and Their Poisoning by Anticancer and Antibacterial Drugs

(2010) Yves Pommier et al.   CHEMISTRY & BIOLOGY

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

A method for genome-wide analysis of DNA helical tension by means of psoralen–DNA photobinding

(2010) Ignacio Bermúdez et al.   NUCLEIC ACIDS RESEARCH

Budding Yeast Wpl1(Rad61)-Pds5 Complex Counteracts Sister Chromatid Cohesion-Establishing Reaction

(2009) Takashi Sutani et al.   CURRENT BIOLOGY

Cohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus

(2009) Raffaella Nativio et al.   PLoS Genetics

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

Tracking single molecules in the live cell plasma membrane—Do’s and Don’t’s

(2008) Stefan Wieser et al.   METHODS

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy

(2008) B. Huang et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY