Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

(2020) Marco Di Stefano et al.   GENETICS

Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation

(2020) Fabian Erdel et al.   MOLECULAR CELL

Nucleolus-associated chromatin domains are maintained under heat stress, despite nucleolar reorganization in Arabidopsis thaliana

(2020) Ariadna Picart-Picolo et al.   JOURNAL OF PLANT RESEARCH

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

(2020) Satish Sati et al.   MOLECULAR CELL

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states

(2020) Hans-Wilhelm Nützmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-contact 3C reveals that the human genome during interphase is largely not entangled

(2020) Filipe Tavares-Cadete et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

(2019) Jonas Paulsen et al.   NATURE GENETICS

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2

(2019) Aaron J. Plys et al.   GENES & DEVELOPMENT

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus

(2019) Jörg Morf et al.   NATURE BIOTECHNOLOGY

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA

(2019) Antonio Valdés et al.   NUCLEIC ACIDS RESEARCH

Unconventional Myosins: How Regulation Meets Function

(2019) Natalia Fili et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Computational 3D genome modeling using Chrom3D

(2018) Jonas Paulsen et al.   Nature Protocols

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes

(2018) Enrique Vidal et al.   NUCLEIC ACIDS RESEARCH

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

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes

(2018) Surya K. Ghosh et al.   PLoS Computational Biology

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

(2018) Quentin Szabo et al.   Science Advances

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

(2018) Huasong Lu et al.   NATURE

Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells

(2018) Jianquan Xu et al.   Cell Reports

Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation

(2018) Shuai Zhao et al.   CELL RESEARCH

Hormone-control regions mediate steroid receptor–dependent genome organization

(2018) François Le Dily et al.   GENOME RESEARCH

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

(2018) Adam Buckle et al.   MOLECULAR CELL

Bottom–up modeling of chromatin segregation due to epigenetic modifications

(2018) Quinn MacPherson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Bogdan Bintu et al.   SCIENCE

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

(2017) Xiuli Bi et al.   GENOME RESEARCH

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

FISH-ing for captured contacts: towards reconciling FISH and 3C

(2017) Geoffrey Fudenberg et al.   NATURE METHODS

DNA knots occur in intracellular chromatin

(2017) Antonio Valdés et al.   NUCLEIC ACIDS RESEARCH

Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus

(2017) Caitlin Hult et al.   NUCLEIC ACIDS RESEARCH

Nonequilibrium Chromosome Looping via Molecular Slip Links

(2017) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

Are There Knots in Chromosomes?

(2017) Jonathan Siebert et al.   Polymers

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

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

(2016) Chang Liu et al.   GENOME RESEARCH

A novel family of plant nuclear envelope-associated proteins

(2016) Vidya Pawar et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2016) Alistair N. Boettiger et al.   NATURE

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Delineation of metabolic gene clusters in plant genomes by chromatin signatures

(2016) Nan Yu et al.   NUCLEIC ACIDS RESEARCH

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

Transferable model for chromosome architecture

(2016) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

(2016) Harianto Tjong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome

(2016) Frédéric Pontvianne et al.   Cell Reports

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome

(2016) Alaguraj Veluchamy et al.   PLoS One

Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization

(2016) Marco Di Stefano et al.   Scientific Reports

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus

(2015) Joana Sequeira-Mendes et al.   CHROMOSOMA

Restraint-based three-dimensional modeling of genomes and genomic domains

(2015) François Serra et al.   FEBS LETTERS

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

(2015) Marie Trussart et al.   NUCLEIC ACIDS RESEARCH

Topology, structures, and energy landscapes of human chromosomes

(2015) Bin Zhang 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

Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana

(2015) Lauriane Simon et al.   Frontiers in Plant Science

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

Genome-wide analysis of local chromatin packing inArabidopsis thaliana

(2014) Congmao Wang et al.   GENOME RESEARCH

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

(2014) J. Sequeira-Mendes et al.   PLANT CELL

From a melt of rings to chromosome territories: the role of topological constraints in genome folding

(2014) Jonathan D Halverson et al.   REPORTS ON PROGRESS IN PHYSICS

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Epigenetic control of RNA polymerase I transcription in mammalian cells

(2012) Ingrid Grummt et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

(2012) Hua Wong et al.   CURRENT BIOLOGY

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

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Chromosome Organization and Dynamics during Interphase, Mitosis, and Meiosis in Plants

(2011) C.-L. Tiang et al.   PLANT PHYSIOLOGY

Organization and dynamics of plant interphase chromosomes

(2011) Ingo Schubert et al.   TRENDS IN PLANT SCIENCE

Looping Probabilities in Model Interphase Chromosomes

(2010) Angelo Rosa et al.   BIOPHYSICAL JOURNAL

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei

(2010) Philippe Andrey et al.   PLoS Computational Biology

Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts

(2010) Ishita S Mehta et al.   GENOME BIOLOGY

Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei

(2009) S. de Nooijer et al.   NUCLEIC ACIDS RESEARCH

Topological origins of chromosomal territories

(2009) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

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

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

The Epigenetics of rRNA Genes: From Molecular to Chromosome Biology

(2008) Brian McStay et al.   Annual Review of Cell and Developmental Biology

Mappingin VivoChromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction

(2008) Job Dekker   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology