Factors and Mechanisms That Influence Chromatin-Mediated Enhancer–Promoter Interactions and Transcriptional Regulation

CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters

(2022) Havva Ortabozkoyun et al.   NATURE GENETICS

Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance

(2022) Jan Padeken et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals

(2022) Aditya Sankar et al.   NATURE GENETICS

Context-specific Polycomb mechanisms in development

(2022) Jongmin J. Kim et al.   NATURE REVIEWS GENETICS

The spatial organization of transcriptional control

(2022) Antonina Hafner et al.   NATURE REVIEWS GENETICS

Supercharging BRD4 with NUT in carcinoma

(2021) Kyle P. Eagen et al.   ONCOGENE

BET inhibition disrupts transcription but retains enhancer-promoter contact

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

ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

(2021) Qiling Zhou et al.   Nature Communications

Pioneering the developmental frontier

(2021) Elizabeth D. Larson et al.   MOLECULAR CELL

H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

(2021) Yichao Cai et al.   Nature Communications

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

Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci

(2021) Stephanie Sungalee et al.   NATURE GENETICS

The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression

(2021) Marios Agelopoulos et al.   Frontiers in Immunology

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development

(2020) Chew Yee Ngan et al.   NATURE GENETICS

Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment

(2020) Celeste D. Rosencrance et al.   MOLECULAR CELL

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

Biomolecular Condensates in the Nucleus

(2020) Benjamin R. Sabari et al.   TRENDS IN BIOCHEMICAL SCIENCES

Pioneer Transcription Factors Initiating Gene Network Changes

(2020) Kenneth S. Zaret   Annual Review of Genetics

Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

(2020) James P. Reddington et al.   DEVELOPMENTAL CELL

Enhancer-promoter communication: hubs or loops?

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

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains

(2019) Maria C. Donaldson-Collier et al.   NATURE GENETICS

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

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

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

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

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

(2019) Laila El Khattabi et al.   CELL

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

(2019) Mustafa Mir et al.   DEVELOPMENT

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

Liquid–liquid phase separation is an intrinsic physicochemical property of chromatin

(2019) Yi Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

(2018) Tahsin Stefan Barakat et al.   Cell Stem Cell

The Yin and Yang of YY1 in tumor growth and suppression

(2018) Levon M. Khachigian   INTERNATIONAL JOURNAL OF CANCER

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

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate

(2018) Alexandre Mayran et al.   NATURE GENETICS

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

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

Dissecting super-enhancer hierarchy based on chromatin interactions

(2018) Jialiang Huang et al.   Nature Communications

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

(2018) Lusy Handoko et al.   Epigenetics

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Nut Directs p300-Dependent, Genome-Wide H4 Hyperacetylation in Male Germ Cells

(2018) Hitoshi Shiota et al.   Cell Reports

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

(2018) Ann Boija et al.   CELL

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

(2018) Natsuhiko Kumasaka et al.   NATURE GENETICS

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan 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

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin looping as a target for altering erythroid gene expression

(2016) Ivan Krivega et al.   Annals of the New York Academy of Sciences

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

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

(2016) Alistair N. Boettiger et al.   NATURE

Histone H3 globular domain acetylation identifies a new class of enhancers

(2016) Madapura M Pradeepa et al.   NATURE GENETICS

BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin

(2016) Ballachanda N Devaiah et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Polycomb in Transcriptional Phase Transition of Developmental Genes

(2016) Takashi Kondo et al.   TRENDS IN BIOCHEMICAL SCIENCES

BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin

(2016) Ballachanda N Devaiah et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains

(2015) Artyom A. Alekseyenko et al.   GENES & DEVELOPMENT

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo 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

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

Polycomb Potentiates Meis2 Activation in Midbrain by Mediating Interaction of the Promoter with a Tissue-Specific Enhancer

(2014) Takashi Kondo et al.   DEVELOPMENTAL CELL

Role of LDB1 in the transition from chromatin looping to transcription activation

(2014) I. Krivega et al.   GENES & DEVELOPMENT

Genome-Scale Acetylation-Dependent Histone Eviction during Spermatogenesis

(2014) Afsaneh Goudarzi et al.   JOURNAL OF MOLECULAR BIOLOGY

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells

(2014) Pierre Therizols et al.   SCIENCE

A bump-and-hole approach to engineer controlled selectivity of BET bromodomain chemical probes

(2014) M. G. J. Baud et al.   SCIENCE

Control of Embryonic Stem Cell Identity by BRD4-Dependent Transcriptional Elongation of Super-Enhancer-Associated Pluripotency Genes

(2014) Raffaella Di Micco et al.   Cell Reports

Embracing change to remain the same: conservation of polycomb functions despite divergence of binding motifs among species

(2013) Jafar Sharif et al.   CURRENT OPINION IN CELL BIOLOGY

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

(2013) Kyoichi Isono et al.   DEVELOPMENTAL CELL

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

(2013) G. C. A. Taylor et al.   GENOME RESEARCH

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

(2013) Eliezer Calo et al.   MOLECULAR CELL

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai 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

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

The Growth-Suppressive Function of the Polycomb Group Protein Polyhomeotic Is Mediated by Polymerization of Its Sterile Alpha Motif (SAM) Domain

(2012) Angela K. Robinson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bromodomain Protein Brd4 Associated with Acetylated Chromatin Is Important for Maintenance of Higher-order Chromatin Structure

(2012) Ranran Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

LIM Domain Binding Proteins 1 and 2 Have Different Oligomeric States

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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Model for all Genomes: The Role of Transcription Factories

(2009) Peter R. Cook   JOURNAL OF MOLECULAR BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Mechanisms of Polycomb gene silencing: knowns and unknowns

(2009) Jeffrey A. Simon et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA