The role of transcription in shaping the spatial organization of the genome

Nuclear pore density controls heterochromatin reorganization during senescence

(2019) Charlene Boumendil et al.   GENES & DEVELOPMENT

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

(2018) Sofia A. Quinodoz et al.   CELL

Dynamic regulation of nucleolar architecture

(2018) Attila Németh et al.   CURRENT OPINION IN CELL BIOLOGY

The Insulator Protein CTCF Is Required for CorrectHoxGene Expression, but Not for Embryonic Development inDrosophila

(2018) Maria Cristina Gambetta et al.   GENETICS

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

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

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

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

SMC Complexes: Universal DNA Looping Machines with Distinct Regulators

(2018) Marjon S. van Ruiten et al.   TRENDS IN GENETICS

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

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

The Insulator Protein CTCF Is Required for CorrectHoxGene Expression, but Not for Embryonic Development inDrosophila

(2018) Maria Cristina Gambetta et al.   GENETICS

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

RNA polymerase II clustering through carboxy-terminal domain phase separation

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

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

(2018) Ann Boija et al.   CELL

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Disruption of the UBF gene induces aberrant somatic nucleolar bodies and disrupts embryo nucleolar precursor bodies

(2017) Nourdine Hamdane et al.   GENE

Comprehensive characterization of neutrophil genome topology

(2017) Yina Zhu et al.   GENES & DEVELOPMENT

Causes and consequences of nuclear gene positioning

(2017) Sigal Shachar et al.   JOURNAL OF CELL SCIENCE

Genetic and epigenetic control of the spatial organization of the genome

(2017) Jason Brickner   MOLECULAR BIOLOGY OF THE CELL

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

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

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Ten principles of heterochromatin formation and function

(2017) Robin C. Allshire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation

(2017) Stefan Dillinger et al.   PLoS One

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

(2017) Sherif El-Sharnouby et al.   PLoS One

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

(2017) Yoon Hee Jung et al.   Cell Reports

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

(2017) Oscar Velazquez Camacho et al.   eLife

CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals

(2017) Mariana Ruiz-Velasco et al.   Cell Systems

Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters

(2017) Kobe C. Yuen et al.   Science Advances

The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome

(2016) Cailyn H. Spurrell et al.   CELL

A Guide to Packing Your DNA

(2016)   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries

(2016) Tung BK Le et al.   EMBO JOURNAL

TALE-light imaging reveals maternally guided, H3K9me2/3-independent emergence of functional heterochromatin inDrosophilaembryos

(2016) Kai Yuan et al.   GENES & DEVELOPMENT

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Chromatin Domains: The Unit of Chromosome Organization

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

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

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

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos

(2016) Patricia Heyn et al.   RNA Biology

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

Spatial segregation of heterochromatin: Uncovering functionality in a multicellular organism

(2016) Daphne S. Cabianca et al.   Nucleus

Spatial segregation of heterochromatin: Uncovering functionality in a multicellular organism

(2016) Daphne S. Cabianca et al.   Nucleus

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Alu element-containing RNAs maintain nucleolar structure and function

(2015) M. Caudron-Herger et al.   EMBO JOURNAL

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

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

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

(2015) Li Li et al.   MOLECULAR CELL

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging

(2015) Martial Marbouty et al.   MOLECULAR CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

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

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

RNAi and Heterochromatin Assembly

(2015) Robert Martienssen et al.   Cold Spring Harbor Perspectives in Biology

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng 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

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT BIOLOGY

High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm

(2014) Benjamin R. Carone et al.   DEVELOPMENTAL CELL

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

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

Functional redundancy in the nuclear compartmentalization of the late-replicating genome

(2014) Tobias Ragoczy et al.   Nucleus

SIR Proteins and the Assembly of Silent Chromatin in Budding Yeast

(2013) Stephanie Kueng et al.   Annual Review of Genetics

Developmentally Regulated Subnuclear Genome Reorganization Restricts Neural Progenitor Competence in Drosophila

(2013) Minoree Kohwi et al.   CELL

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

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

(2013) Jennifer E. Phillips-Cremins 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

Cohesin-mediated interactions organize chromosomal domain architecture

(2013) Sevil Sofueva et al.   EMBO JOURNAL

Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes

(2013) E. Lund et al.   GENOME RESEARCH

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

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

(2013) G. Andrey et al.   SCIENCE

Organization of the Mitotic Chromosome

(2013) N. Naumova 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

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   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

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes

(2011) C. P. Brangwynne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

(2011) Bas Tolhuis et al.   PLoS Genetics

Nucleoporins Directly Stimulate Expression of Developmental and Cell-Cycle Genes Inside the Nucleoplasm

(2010) Bernike Kalverda et al.   CELL

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

A Strand-Specific Burst in Transcription of Pericentric Satellites Is Required for Chromocenter Formation and Early Mouse Development

(2010) Aline.V. Probst et al.   DEVELOPMENTAL CELL

Hsp70 gene association with nuclear speckles is Hsp70 promoter specific

(2010) Yan Hu et al.   JOURNAL OF CELL BIOLOGY

High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

(2010) Silvana van Koningsbruggen et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

(2010) Joke G. van Bemmel et al.   PLoS One

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution

(2009) Irina Solovei et al.   CELL

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

The LPS-Induced Transcriptional Upregulation of the Chicken Lysozyme Locus Involves CTCF Eviction and Noncoding RNA Transcription

(2008) Pascal Lefevre et al.   MOLECULAR CELL

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

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

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