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

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

(2019) Kevin Monahan et al.   NATURE

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

(2018) Sofia A. Quinodoz et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells

(2018) Gangqing Hu et al.   IMMUNITY

Visualizing transcription factor dynamics in living cells

(2018) Zhe Liu et al.   JOURNAL OF CELL BIOLOGY

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types

(2018) Anne Zirkel et al.   MOLECULAR 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

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

(2018) Shasha Chong et al.   SCIENCE

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu 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

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

(2018) James H. Sun et al.   CELL

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

(2018) Glòria Mas et al.   NATURE GENETICS

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

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

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

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

(2018) Ann Boija et al.   CELL

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang 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

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

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

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

(2018) Aleksandra Pękowska et al.   Cell Systems

Clustering of Drosophila housekeeping promoters facilitates their expression

(2017) Marc Corrales et al.   GENOME RESEARCH

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

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

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

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

(2017) Ilya M. Flyamer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling

(2017) Hui Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung et al.   Cell Reports

Recent evidence that TADs and chromatin loops are dynamic structures

(2017) Anders S. Hansen et al.   Nucleus

Recent evidence that TADs and chromatin loops are dynamic structures

(2017) Anders S. Hansen et al.   Nucleus

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   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

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

(2016) Peter Hugo Lodewijk Krijger et al.   Cell Stem Cell

Liquid-like behavior of chromatin

(2016) Kazuhiro Maeshima et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments

(2016) Patrick J. Wijchers et al.   MOLECULAR CELL

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

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

Exploring chromatin organization mechanisms through its dynamic properties

(2016) Irena Bronshtein et al.   Nucleus

Exploring chromatin organization mechanisms through its dynamic properties

(2016) Irena Bronshtein et al.   Nucleus

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

Characterization and dynamics of pericentromere-associated domains in mice

(2015) Patrick J. Wijchers et al.   GENOME RESEARCH

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

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

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

(2015) Jennifer C. Harr et al.   JOURNAL OF CELL BIOLOGY

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

(2015) James Fraser et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje 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

Clustering of mammalianHoxgenes with other H3K27me3 targets within an active nuclear domain

(2015) Maxence Vieux-Rochas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Control of developmentally primed erythroid genes by combinatorial co-repressor actions

(2015) Ralph Stadhouders et al.   Nature Communications

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

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

(2014) Jill M. Dowen 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

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

(2014) Pierre Therizols et al.   SCIENCE

Pre-B Cell Receptor Signaling Induces Immunoglobulin κ Locus Accessibility by Functional Redistribution of Enhancer-Mediated Chromatin Interactions

(2014) Ralph Stadhouders et al.   PLOS BIOLOGY

3D imaging of Sox2 enhancer clusters in embryonic stem cells

(2014) Zhe Liu et al.   eLife

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

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

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

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

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

Identical cells with different 3D genomes; cause and consequences?

(2013) Peter HL Krijger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

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

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

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

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

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

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

The DNA-Binding Protein CTCF Limits Proximal Vκ Recombination and Restricts κ Enhancer Interactions to the Immunoglobulin κ Light Chain Locus

(2011) Claudia Ribeiro de Almeida et al.   IMMUNITY

CTCF-binding elements mediate control of V(D)J recombination

(2011) Chunguang Guo et al.   NATURE

Variegated gene expression caused by cell-specific long-range DNA interactions

(2011) Daan Noordermeer et al.   NATURE CELL BIOLOGY

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

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

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

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

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

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

(2008) Suchit Jhunjhunwala et al.   CELL

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

(2008) Effie Apostolou et al.   CELL

Transcription factories are nuclear subcompartments that remain in the absence of transcription

(2008) J. A. Mitchell et al.   GENES & DEVELOPMENT

Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription

(2008) Robert-Jan Palstra et al.   PLoS One