Dynamics of transcriptional enhancers and chromosome topology in gene regulation

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

(2018) James H. Sun et al.   CELL

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

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

(2018) Bogdan Bintu et al.   SCIENCE

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

(2018) Jeremy Dufourt et al.   Nature Communications

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

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

(2017) Georg A. Busslinger et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

The condensin complex is a mechanochemical motor that translocates along DNA

(2017) Tsuyoshi Terakawa et al.   SCIENCE

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

(2016) Emily M. Smith et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

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

(2016) Iain F Davidson et al.   EMBO JOURNAL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz 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

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei

(2016) T. Niroshini Senaratne et al.   PLoS Genetics

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

(2016) Miki Fujioka et al.   PLoS Genetics

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

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

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

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

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

(2014) Suhas S.P. Rao et al.   CELL

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

(2013) Bjoern Chapuy et al.   CANCER CELL

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation

(2013) J. Shi et al.   GENES & DEVELOPMENT

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

The Drosophila eve Insulator Homie Promotes eve Expression and Protects the Adjacent Gene from Repression by Polycomb Spreading

(2013) Miki Fujioka et al.   PLoS Genetics

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

(2012) Tom Sexton et al.   CELL

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

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Visualization of Individual Scr mRNAs during Drosophila Embryogenesis Yields Evidence for Transcriptional Bursting

(2009) Adam Paré et al.   CURRENT BIOLOGY

A chromatin insulator mediates transgene homing and very long-range enhancer-promoter communication

(2009) M. Fujioka et al.   DEVELOPMENT

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The RNA polymerase II core promoter — the gateway to transcription

(2008) Tamar Juven-Gershon et al.   CURRENT OPINION IN CELL BIOLOGY

Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA