Coming full circle: On the origin and evolution of the looping model for enhancer–promoter communication

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

(2022) Lesly Calderon et al.   eLife

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

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

(2021) Naoki Kubo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhancers predominantly regulate gene expression during differentiation via transcription initiation

(2021) Martin S.C. Larke et al.   MOLECULAR CELL

Structure of the human Mediator-bound transcription preinitiation complex

(2021) R. Abdella et al.   SCIENCE

Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

(2021) Jing Luan et al.   Cell Reports

Structures of the human Mediator and Mediator-bound preinitiation complex

(2021) Xizi Chen et al.   SCIENCE

Enhancer release and retargeting activates disease-susceptibility genes

(2021) Soohwan Oh et al.   NATURE

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

(2020) Elena M. Pugacheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

(2020) Gordana Wutz et al.   eLife

Cryo-EM structure of the human cohesin-NIPBL-DNA complex

(2020) Zhubing Shi et al.   SCIENCE

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

(2020) Grégoire Stik et al.   NATURE GENETICS

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

(2020) Jennifer M. Luppino et al.   NATURE GENETICS

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

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

WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation

(2020) Ning Qing Liu et al.   NATURE GENETICS

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

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

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

(2019) Alexandra Despang et al.   NATURE GENETICS

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

(2019) Ji Hun Kim et al.   NATURE METHODS

Absolute quantification of cohesin, CTCF and their regulators in human cells

(2019) Johann Holzmann et al.   eLife

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

(2019) Laila El Khattabi et al.   CELL

The expanding phenotypes of cohesinopathies: one ring to rule them all!

(2019) Jessica Piché et al.   CELL CYCLE

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

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

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

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

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

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

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

(2018) Sofia A. Quinodoz et al.   CELL

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans

(2018) Pei-Fang Tsai et al.   MOLECULAR CELL

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

(2018) Aleksandar Kojic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2018) Benjamin R. Sabari et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

(2018) Aleksandar Kojic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

Global transcriptional activity dynamics reveal functional enhancer RNAs

(2018) Yoon Jung Kim et al.   GENOME RESEARCH

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

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

Gene Therapy for β-Hemoglobinopathies

(2017) Marina Cavazzana et al.   MOLECULAR THERAPY

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

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

SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development

(2017) Tomoko Sagai et al.   Scientific Reports

Glucocorticoid Receptor Binding Induces Rapid and Prolonged Large-Scale Chromatin Decompaction at Multiple Target Loci

(2017) Alasdair W. Jubb et al.   Cell Reports

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Cohesin Releases DNA through Asymmetric ATPase-Driven Ring Opening

(2016) Ahmed M.O. Elbatsh et al.   MOLECULAR 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

Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin

(2016) Kyoko Hiragami-Hamada et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

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

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

(2015) Evangelos Pefanis et al.   CELL

The Isl1/Ldb1 Complex Orchestrates Genome-wide Chromatin Organization to Instruct Differentiation of Multipotent Cardiac Progenitors

(2015) Luca Caputo et al.   Cell Stem Cell

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

The Mediator complex: a central integrator of transcription

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

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

(2015) Roland Jäger et al.   Nature Communications

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions

(2014) Joseph S. Lucas 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

Structure of Yin Yang 1 Oligomers That Cooperate with RuvBL1-RuvBL2 ATPases

(2014) Andrés López-Perrote et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Closing the cohesin ring: Structure and function of its Smc3-kleisin interface

(2014) T. G. Gligoris et al.   SCIENCE

Function of YY1 in Long-Distance DNA Interactions

(2014) Michael L. Atchison   Frontiers in Immunology

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

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

The DNA-binding factor Ctcf critically controls gene expression in macrophages

(2013) Tatjana Nikolic et al.   Cellular & Molecular Immunology

YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus

(2013) Xuan Pan et al.   EMBO JOURNAL

Flexible Long-Range Loops in the VH Gene Region of the Igh Locus Facilitate the Generation of a Diverse Antibody Repertoire

(2013) Jasna Medvedovic et al.   IMMUNITY

A novel regulatory element for Shh expression in the lung and gut of mouse embryos

(2013) Nagaharu Tsukiji et al.   MECHANISMS OF DEVELOPMENT

Occupying Chromatin: Polycomb Mechanisms for Getting to Genomic Targets, Stopping Transcriptional Traffic, and Staying Put

(2013) Jeffrey A. Simon et al.   MOLECULAR CELL

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Wapl is an essential regulator of chromatin structure and chromosome segregation

(2013) Antonio Tedeschi et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

The Switch from Fetal to Adult Hemoglobin

(2013) V. G. Sankaran et al.   Cold Spring Harbor Perspectives in Medicine

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

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

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

Noncoding transcription within the Igh distal VH region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

(2012) J. Verma-Gaur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vitro loading of human cohesin on DNA by the human Scc2-Scc4 loader complex

(2012) V. P. Bermudez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin: a catenase with separate entry and exit gates?

(2011) Kim Nasmyth   NATURE CELL BIOLOGY

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

The role of Drosophila Lamin C in muscle function and gene expression

(2010) G. Dialynas et al.   DEVELOPMENT

LIM Domain Binding Proteins 1 and 2 Have Different Oligomeric States

(2010) Arwen J. Cross et al.   JOURNAL OF MOLECULAR BIOLOGY

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

Active RNA Polymerases: Mobile or Immobile Molecular Machines?

(2010) Argyris Papantonis et al.   PLOS BIOLOGY

Histone Crosstalk between H3S10ph and H4K16ac Generates a Histone Code that Mediates Transcription Elongation

(2009) Alessio Zippo et al.   CELL

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Induced Chromosomal Proximity and Gene Fusions in Prostate Cancer

(2009) R.-S. Mani et al.   SCIENCE

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

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

Sister Chromatid Cohesion: A Simple Concept with a Complex Reality

(2008) Itay Onn et al.   Annual Review of Cell and Developmental Biology

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence

(2008) R. Ileng Kumaran et al.   JOURNAL OF CELL BIOLOGY

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics