The spatial organization of transcriptional control

Genome organization controls transcriptional dynamics during development

(2022) Philippe J. Batut et al.   SCIENCE

Transcriptional coupling of distant regulatory genes in living embryos

(2022) Michal Levo et al.   NATURE

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

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

(2022) Abrar Aljahani et al.   Nature Communications

Genome oligopaint via local denaturation fluorescence in situ hybridization

(2021) Yanbo Wang et al.   MOLECULAR CELL

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA

(2021) Leslie J. Mateo et al.   Nature Protocols

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

HP1 drives de novo 3D genome reorganization in early Drosophila embryos

(2021) Fides Zenk et al.   NATURE

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

Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue

(2021) Miao Liu et al.   Nature Protocols

Understanding 3D genome organization by multidisciplinary methods

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

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

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

Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions

(2021) Leonid Mirny et al.   Cold Spring Harbor Perspectives in Biology

Uncovering the Principles of Genome Folding by 3D Chromatin Modeling

(2021) Asli Yildirim et al.   Cold Spring Harbor Perspectives in Biology

Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact

(2021) Aparna R. Rajpurkar et al.   Nature Communications

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

Cell-type specialization is encoded by specific chromatin topologies

(2021) Warren Winick-Ng et al.   NATURE

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

(2021) Yodai Takei et al.   SCIENCE

The CBX family of proteins in transcriptional repression and memory

(2020) Jongmin Kim et al.   JOURNAL OF BIOSCIENCES

Phase-separation in chromatin organization

(2020) Geeta J Narlikar   JOURNAL OF BIOSCIENCES

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

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M

(2020) Andrés M. Cardozo Gizzi et al.   Nature Protocols

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

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

3D ATAC-PALM: super-resolution imaging of the accessible genome

(2020) Liangqi Xie et al.   NATURE METHODS

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

(2020) Jonathan A. Beagan et al.   NATURE NEUROSCIENCE

Chromosomes Phase Transition to Function

(2020) Mario Nicodemi et al.   BIOPHYSICAL JOURNAL

Three-dimensional chromatin in disease: What holds us together and what drives us apart?

(2020) Daniel M. Ibrahim et al.   CURRENT OPINION IN CELL BIOLOGY

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields

(2020) Andrews Akwasi Agbleke et al.   MOLECULAR CELL

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

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

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

(2020) Mattia Conte et al.   Nature Communications

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

(2020) Miao Liu et al.   Nature Communications

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

(2020) Jun-Han Su et al.   CELL

Regulation of single-cell genome organization into TADs and chromatin nanodomains

(2020) Quentin Szabo et al.   NATURE GENETICS

Multi-contact 3C reveals that the human genome during interphase is largely not entangled

(2020) Filipe Tavares-Cadete et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The macro and micro of chromosome conformation capture

(2020) Viraat Y. Goel et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Enhancer-promoter communication: hubs or loops?

(2020) Bomyi Lim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE 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

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

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

(2019) Jeffrey M Alexander et al.   eLife

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D

(2019) Michael I. Robson et al.   MOLECULAR CELL

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang 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

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

(2019) Nimish Khanna et al.   Nature Communications

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

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

Genomic methods in profiling DNA accessibility and factor localization

(2019) David C. Klein et al.   CHROMOSOME RESEARCH

The multiscale effects of polycomb mechanisms on 3D chromatin folding

(2019) Thierry Cheutin et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

(2019) A. Marieke Oudelaar et al.   Nature Communications

Defining Functionally Relevant Spatial Chromatin Domains: It is a TAD Complicated

(2019) Natalia Sikorska et al.   JOURNAL OF MOLECULAR BIOLOGY

TADs and Their Borders: Free Movement or Building a Wall?

(2019) Li-Hsin Chang et al.   JOURNAL OF MOLECULAR BIOLOGY

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL 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

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

(2018) Benjamin R. Sabari et al.   SCIENCE

3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering

(2018) Jinlei Han et al.   Molecular Cytogenetics

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Visualizing and discovering cellular structures with super-resolution microscopy

(2018) Yaron M. Sigal et al.   SCIENCE

Interphase human chromosome exhibits out of equilibrium glassy dynamics

(2018) Guang Shi et al.   Nature Communications

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

(2018) Jill M. Brown et al.   Nature Communications

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

(2018) A. Marieke Oudelaar et al.   NATURE GENETICS

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

Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases

(2018) Marc S. Halfon   TRENDS IN GENETICS

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

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

(2017) Ilya M. Flyamer et al.   NATURE

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

(2017) Takashi Nagano et al.   NATURE

Promoting transcription over long distances

(2017) Rui R Catarino et al.   NATURE GENETICS

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

FISH-ing for captured contacts: towards reconciling FISH and 3C

(2017) Geoffrey Fudenberg et al.   NATURE METHODS

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

Chromosome conformation capture technologies and their impact in understanding genome function

(2016) Satish Sati et al.   CHROMOSOMA

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

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

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

(2016) Alistair N. Boettiger et al.   NATURE

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

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

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

(2016) Miki Fujioka et al.   PLoS Genetics

An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/Ptch1

(2016) David S Lorberbaum et al.   eLife

Functional role of dimerization and CP190 interacting domains of CTCF protein in Drosophila melanogaster

(2015) Artem Bonchuk et al.   BMC BIOLOGY

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

(2015) Darío G. Lupiáñez et al.   CELL

The open for business model of the bithorax complex in Drosophila

(2015) Robert K. Maeda et al.   CHROMOSOMA

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

(2015) Wulan Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine 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

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

REGULATION OF GENE EXPRESSION IN THE GENOMIC CONTEXT

(2014) Taylor J Atkinson et al.   Computational and Structural Biotechnology Journal

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Making connections: Insulators organize eukaryotic chromosomes into independent cis-regulatory networks

(2013) Darya Chetverina et al.   BIOESSAYS

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

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

(2012) Wulan Deng et al.   CELL

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

(2012) Tom Sexton et al.   CELL

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

(2012) Guoliang Li et al.   CELL

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

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

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells

(2010) Bo Huang et al.   CELL

A guide to super-resolution fluorescence microscopy

(2010) Lothar Schermelleh et al.   JOURNAL OF CELL BIOLOGY

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Thermodynamic Pathways to Genome Spatial Organization in the Cell Nucleus

(2009) Mario Nicodemi et al.   BIOPHYSICAL JOURNAL

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

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

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

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL