3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

Genome organization controls transcriptional dynamics during development

(2022) Philippe J. Batut et al.   SCIENCE

Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos

(2022) Chen C. Li et al.   Nature Communications

Regulating specificity in enhancer–promoter communication

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

Transcription activation is enhanced by multivalent interactions independent of phase separation

(2022) Jorge Trojanowski et al.   MOLECULAR CELL

Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription

(2022) Shasha Chong et al.   MOLECULAR CELL

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

MCM complexes are barriers that restrict cohesin-mediated loop extrusion

(2022) Bart J. H. Dequeker et al.   NATURE

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

(2022) Aditya S. Deshpande et al.   NATURE BIOTECHNOLOGY

NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency

(2022) Kyoung-Jae Choi et al.   NATURE CELL BIOLOGY

Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome

(2022) Joanna W. Jachowicz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation

(2022) Katerina Kraft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2022) Michele Gabriele et al.   SCIENCE

Cohesin-dependence of neuronal gene expression relates to chromatin loop length

(2022) Lesly Calderon et al.   eLife

The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation

(2022) Lorenzo Rinaldi et al.   Science Advances

TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors

(2022) Wenliang Wang et al.   NATURE IMMUNOLOGY

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

(2022) Niels J. Rinzema et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SMC complexes can traverse physical roadblocks bigger than their ring size

(2022) Biswajit Pradhan et al.   Cell Reports

Enhancer redundancy in development and disease

(2021) Evgeny Z. Kvon et al.   NATURE REVIEWS GENETICS

BET inhibition disrupts transcription but retains enhancer-promoter contact

(2021) Nicholas T. Crump et al.   Nature Communications

Phase separation of DNA: from past to present

(2021) John T. King et al.   BIOPHYSICAL JOURNAL

Base-resolution models of transcription-factor binding reveal soft motif syntax

(2021) Žiga Avsec et al.   NATURE GENETICS

Structure of the human Mediator-bound transcription preinitiation complex

(2021) R. Abdella et al.   SCIENCE

H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization

(2021) Bobbie Pelham-Webb et al.   MOLECULAR CELL

Suppression of liquid–liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells

(2021) Sergey V Ulianov et al.   NUCLEIC ACIDS RESEARCH

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

(2021) Jinmi Choi et al.   eLife

The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter–enhancer looping

(2021) Fei Sun et al.   GENES & DEVELOPMENT

Defining genome architecture at base-pair resolution

(2021) Peng Hua et al.   NATURE

Single-cell measurement of higher-order 3D genome organization with scSPRITE

(2021) Mary V. Arrastia et al.   NATURE BIOTECHNOLOGY

Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization

(2021) Rajesh Sharma et al.   Nature Communications

Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath

(2021) Xingjie Ren et al.   Science Advances

Cohesin mediates DNA loop extrusion by a “swing and clamp” mechanism

(2021) Benedikt W. Bauer et al.   CELL

Xist nucleates local protein gradients to propagate silencing across the X chromosome

(2021) Yolanda Markaki et al.   CELL

Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions

(2021) Jia Wang et al.   Cell Stem Cell

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

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

Tcf1 and Lef1 provide constant supervision to mature CD8+ T cell identity and function by organizing genomic architecture

(2021) Qiang Shan et al.   Nature Communications

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis

(2021) Shu Zhang et al.   Science Advances

On the existence and functionality of topologically associating domains

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

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Selective Mediator dependence of cell-type-specifying transcription

(2020) Martin G. Jaeger et al.   NATURE GENETICS

Transcription factors: building hubs in the 3D space

(2020) Dafne Campigli Di Giammartino et al.   CELL CYCLE

Loop extrusion: theory meets single-molecule experiments

(2020) Edward J. Banigan et al.   CURRENT OPINION IN CELL BIOLOGY

CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies

(2020) Woonyung Hur et al.   DEVELOPMENTAL CELL

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

(2020) Michiel J. Thiecke et al.   Cell Reports

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

(2020) Jun-Han Su et al.   CELL

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

(2020) Jieru Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic

(2020) Rachel Waymack et al.   eLife

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency

(2020) Bobbie Pelham-Webb et al.   Stem Cell Reports

Enhancer-promoter communication: hubs or loops?

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

LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice

(2019) Kevin Monahan et al.   NATURE

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

(2019) Leslie J. Mateo et al.   NATURE

Multiplex chromatin interactions with single-molecule precision

(2019) Meizhen Zheng et al.   NATURE

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

(2019) Jelena Petrovic et al.   MOLECULAR CELL

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

(2019) Joke G. van Bemmel et al.   NATURE GENETICS

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Advancements in mapping 3D genome architecture

(2019) Daniel J. McKay et al.   METHODS

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

(2019) Irene Miguel-Escalada et al.   NATURE GENETICS

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

The Cornelia de Lange Syndrome-associated factor NIPBL interacts with BRD4 ET domain for transcription control of a common set of genes

(2019) Noelia Luna-Peláez et al.   Cell Death & Disease

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

(2019) Christopher Barrington et al.   Nature Communications

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

(2019) Laila El Khattabi et al.   CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks

(2019) Dafne Campigli Di Giammartino et al.   NATURE CELL BIOLOGY

RNA polymerases as moving barriers to condensin loop extrusion

(2019) Hugo B. Brandão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   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

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

Organization of Chromosomal DNA by SMC Complexes

(2019) Stanislau Yatskevich et al.   Annual Review of Genetics

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation

(2018) Adam G. Larson et al.   BIOCHEMISTRY

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

(2018) Sofia A. Quinodoz et al.   CELL

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange–like syndrome

(2018) Gabrielle Olley et al.   NATURE GENETICS

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

Widespread Enhancer Activity from Core Promoters

(2018) Alejandra Medina-Rivera et al.   TRENDS IN BIOCHEMICAL SCIENCES

Dissecting super-enhancer hierarchy based on chromatin interactions

(2018) Jialiang Huang et al.   Nature Communications

Interchromosomal interactions: A genomic love story of kissing chromosomes

(2018) Philipp G. Maass et al.   JOURNAL OF CELL BIOLOGY

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

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

(2018) Ann Boija et al.   CELL

Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods

(2018) Fei Sun et al.   MOLECULAR CELL

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

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

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

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

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

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

(2017) Georg A. Busslinger et al.   NATURE

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration

(2017) Debbie L.C. van den Berg et al.   NEURON

LDB1-mediated enhancer looping can be established independent of mediator and cohesin

(2017) Ivan Krivega et al.   NUCLEIC ACIDS RESEARCH

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map

(2017) Kyle P. Eagen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz 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

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis

(2016) Jialiang Huang et al.   DEVELOPMENTAL CELL

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

(2016) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6

(2016) Barbora Antosova et al.   PLoS Genetics

Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

(2015) Sigal Shachar et al.   CELL

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

(2015) Jacques P Bothma et al.   eLife

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

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

(2014) Yad Ghavi-Helm et al.   NATURE

Chromosomal Contact Permits Transcription between Coregulated Genes

(2013) Stephanie Fanucchi et al.   CELL

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

Direct Interaction of RNA Polymerase II and Mediator Required for Transcription in Vivo

(2011) J. Soutourina et al.   SCIENCE

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Interchromosomal association and gene regulation in trans

(2010) Adam Williams et al.   TRENDS IN GENETICS

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE