Transcription factors: building hubs in the 3D space

On the existence and functionality of topologically associating domains

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

Integrative prediction of gene expression with chromatin accessibility and conformation data

(2020) Florian Schmidt et al.   Epigenetics & Chromatin

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

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

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

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

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

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance

(2019) Jessica A. Bertolini et al.   Cell Stem Cell

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

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

(2019) Ralph Stadhouders et al.   NATURE

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Targeting Super-Enhancers as a Therapeutic Strategy for Cancer Treatment

(2019) Yi He et al.   Frontiers in Pharmacology

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

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

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

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

(2019) Michael Song et al.   NATURE GENETICS

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

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

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

(2019) Christopher Barrington et al.   Nature Communications

Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification

(2019) Alessandro Magli et al.   Nature Communications

Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping

(2019) Masataka Kikuchi et al.   BMC Medical Genomics

Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation

(2019) Aaron D. Viny et al.   Cell Stem Cell

Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells

(2019) Vijay Ramani et al.   METHODS

Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism

(2019) Liang Wang et al.   MOLECULAR CELL

Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation

(2019) Alessandra Dall’Agnese et al.   MOLECULAR CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen 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

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications

(2019) Andrew R. Morton et al.   CELL

Distinct IL‐1α‐responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner

(2019) Sinah‐Sophia Weiterer et al.   EMBO JOURNAL

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

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

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

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

(2018) Sofia A. Quinodoz et al.   CELL

Forces driving the three‐dimensional folding of eukaryotic genomes

(2018) Alvaro Rada‐Iglesias et al.   Molecular Systems Biology

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

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

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

(2018) Archa H. Fox et al.   TRENDS IN BIOCHEMICAL SCIENCES

Extrusion without a motor: a new take on the loop extrusion model of genome organization

(2018) C. A. Brackley et al.   Nucleus

Extrusion without a motor: a new take on the loop extrusion model of genome organization

(2018) C. A. Brackley et al.   Nucleus

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

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

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Trac-looping measures genome structure and chromatin accessibility

(2018) Binbin Lai et al.   NATURE METHODS

A novel enhancer regulates MGMT expression and promotes temozolomide resistance in glioblastoma

(2018) Xiaoyue Chen et al.   Nature Communications

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

(2018) Jiao Sima et al.   CELL

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

(2018) Ann Boija et al.   CELL

Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

(2018) Roubina Tatavosian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Transcription-factor-mediated supervision of global genome architecture maintains B cell identity

(2018) Timothy M. Johanson et al.   NATURE IMMUNOLOGY

OncoBase: a platform for decoding regulatory somatic mutations in human cancers

(2018) Xianfeng Li et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

(2017) Georg A. Busslinger et al.   NATURE

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

(2017) Qin Cao 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

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

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

(2016) Rongxin Fang et al.   CELL RESEARCH

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming

(2016) Jonathan A. Beagan et al.   Cell Stem Cell

A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

(2016) Chris C.-S. Hsiung et al.   GENES & DEVELOPMENT

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

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

(2016) Deborah Hay et al.   NATURE GENETICS

Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2

(2016) Victoria Hung et al.   Nature Protocols

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

(2016) Tingting Jiang et al.   NUCLEIC ACIDS RESEARCH

High-resolution interrogation of functional elements in the noncoding genome

(2016) N. E. Sanjana et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

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

(2015) Darío G. Lupiáñez et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

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

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

(2015) James O J Davies et al.   NATURE METHODS

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

(2015) Takashi Nagano et al.   Nature Protocols

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

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application

(2015) Guoliang Li et al.   BMC GENOMICS

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

(2014) Eirene Markenscoff-Papadimitriou 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

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

(2014) Jill M. Dowen et al.   CELL

The 3D Genome in Transcriptional Regulation and Pluripotency

(2014) David U. Gorkin et al.   Cell Stem Cell

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Rearranging the chromatin for pluripotency

(2013) Francesco Ferrari et al.   CELL CYCLE

Genome organization by Klf4 regulates transcription in pluripotent stem cells

(2013) David Huang et al.   CELL CYCLE

Chromatin looping is needed for iPSC induction

(2013) Ji-Fan Hu et al.   CELL CYCLE

Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

(2013) Zong Wei et al.   Cell Stem 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

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Wulan Deng et al.   CELL

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

(2012) Guoliang Li et al.   CELL

Oncogenic transcription factors as master regulators of chromatin topology

(2012) Olivier Elemento et al.   CELL CYCLE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding

(2012) S.-i. Takebayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

(2011) Anja Nitzsche et al.   PLoS One

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

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

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

Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression

(2008) Effie Apostolou et al.   CELL