Single-gene imaging links genome topology, promoter–enhancer communication and transcription control

A complex regulatory landscape involved in the development of mammalian external genitals

(2020) Ana Rita Amândio et al.   eLife

Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems

(2019) Longzhi Tan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells

(2019) Jieru Li et al.   CELL

LADL: light-activated dynamic looping for endogenous gene expression control

(2019) Ji Hun Kim et al.   NATURE METHODS

Large distances separate coregulated genes in living Drosophila embryos

(2019) Tyler Heist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

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

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci

(2017) Ziying Liu et al.   MOLECULAR CELL

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

(2017) Stefanie L. Morgan et al.   Nature Communications

Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry

(2016) Guanshi Wang et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

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

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

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

Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors

(2016) Muhammad A. Zabidi et al.   TRENDS IN GENETICS

A short G1 phase imposes constitutive replication stress and fork remodelling in mouse embryonic stem cells

(2016) Akshay K. Ahuja et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

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

(2015) Jonathan B Grimm et al.   NATURE METHODS

Simultaneous live imaging of the transcription and nuclear position of specific genes

(2015) Hiroshi Ochiai et al.   NUCLEIC ACIDS RESEARCH

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

(2014) Eirene Markenscoff-Papadimitriou 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

ASox2distal enhancer cluster regulates embryonic stem cell differentiation potential

(2014) Harry Y. Zhou et al.   GENES & DEVELOPMENT

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

(2014) Yan Li et al.   PLoS One

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

(2014) Hiroshi Ochiai et al.   Scientific Reports

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

(2013) Warren A. Whyte et al.   CELL

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

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

In vivo live imaging of RNA polymerase II transcription factories in primary cells

(2013) A. Ghamari et al.   GENES & DEVELOPMENT

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Human Epigenome Browser at Washington University

(2011) Xin Zhou et al.   NATURE METHODS

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY