Recent progress and challenges in single-cell imaging of enhancer–promoter interaction

CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles

(2023) Gabriel R. Cavalheiro et al.   Science Advances

Regulating specificity in enhancer–promoter communication

(2022) Charalampos Chrysovalantis Galouzis et al.   CURRENT OPINION IN CELL BIOLOGY

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

(2022) Michele Gabriele et al.   SCIENCE

Essential role of Cp190 in physical and regulatory boundary formation

(2022) Anjali Kaushal et al.   Science Advances

The spatial organization of transcriptional control

(2022) Antonina Hafner et al.   NATURE REVIEWS GENETICS

Cohesin and CTCF control the dynamics of chromosome folding

(2022) Pia Mach et al.   NATURE GENETICS

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?

(2021) Gabriel R Cavalheiro et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

(2021) Sergio Martin Espinola et al.   NATURE GENETICS

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

(2021) Hui Huang et al.   NATURE GENETICS

Understanding 3D genome organization by multidisciplinary methods

(2021) Ivana Jerkovic´ et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Deletion of CTCF sites in the SHH locus alters enhancer–promoter interactions and leads to acheiropodia

(2021) Aki Ushiki et al.   Nature Communications

New insights into promoter–enhancer communication mechanisms revealed by dynamic single-molecule imaging

(2021) Jieru Li et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

mSWI/SNF promotes Polycomb repression both directly and through genome-wide redistribution

(2021) Christopher M. Weber et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Impact of Space and Time on the Functional Output of the Genome

(2021) Marcelo Nollmann et al.   Cold Spring Harbor Perspectives in Biology

How subtle changes in 3D structure can create large changes in transcription

(2021) Jordan Yupeng Xiao et al.   eLife

The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

(2021) Jonathan P. Karr et al.   GENES & DEVELOPMENT

Single-cell nuclear architecture across cell types in the mouse brain

(2021) Yodai Takei et al.   SCIENCE

Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication

(2020) Moe Yokoshi et al.   MOLECULAR CELL

Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos

(2020) Ahilya N. Sawh et al.   MOLECULAR CELL

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

Monitoring the spatio-temporal organization and dynamics of the genome

(2020) Haitham A Shaban et al.   NUCLEIC ACIDS RESEARCH

Advances in Chromatin Imaging at Kilobase-Scale Resolution

(2020) Alistair Boettiger et al.   TRENDS IN GENETICS

The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization

(2020) Daniel M Ibrahim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields

(2020) Andrews Akwasi Agbleke et al.   MOLECULAR CELL

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

(2020) Jun-Han Su et al.   CELL

Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging

(2020) Hugo B. Brandão et al.   CURRENT OPINION IN CELL BIOLOGY

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

Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

(2019) Judith Hyle et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Jeffrey M Alexander et al.   eLife

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

A genome disconnect

(2019) Elizabeth H. Finn et al.   NATURE GENETICS

Preformed chromatin topology assists transcriptional robustness of Shh during limb development

(2019) Christina Paliou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions

(2019) Nimish Khanna et al.   Nature Communications

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

(2019) Mustafa Mir et al.   DEVELOPMENT

Molecular basis and biological function of variability in spatial genome organization

(2019) Elizabeth H. Finn et al.   SCIENCE

Higher-Order Chromosomal Structures Mediate Genome Function

(2019) Ivana Jerković et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2018) Bo Gu et al.   SCIENCE

Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism

(2018) Jurian Schuijers et al.   Cell Reports

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

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

(2018) Bogdan Bintu et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR 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

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti 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

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

(2012) Elphège P. Nora et al.   NATURE

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH