Integrative studies of 3D genome organization and chromatin structure

LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions

(2022) Helle Lybæk et al.   Autism Research

CENP-B-mediated DNA loops regulate activity and stability of human centromeres

(2022) Florian Chardon et al.   MOLECULAR CELL

Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

(2022) Michele Gabriele et al.   SCIENCE

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

(2021) Marco Di Stefano et al.   NUCLEIC ACIDS RESEARCH

Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome

(2021) J. Yuyang Lu et al.   CELL RESEARCH

Loop extrusion as a mechanism for formation of DNA damage repair foci

(2021) Coline Arnould et al.   NATURE

HP1 drives de novo 3D genome reorganization in early Drosophila embryos

(2021) Fides Zenk et al.   NATURE

Understanding 3D genome organization by multidisciplinary methods

(2021) Ivana Jerkovic´ et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA-loop-extruding SMC complexes can traverse one another in vivo

(2021) Hugo B. Brandão et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Three-dimensional genome organization via triplex-forming RNAs

(2021) Irene Farabella et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-cell nuclear architecture across cell types in the mouse brain

(2021) Yodai Takei et al.   SCIENCE

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

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

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

(2020) Satish Sati et al.   MOLECULAR CELL

Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

(2020) Marco Di Stefano et al.   Nature Communications

Loop extrusion: theory meets single-molecule experiments

(2020) Edward J. Banigan et al.   CURRENT OPINION IN CELL BIOLOGY

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

(2020) Huy Q. Nguyen et al.   NATURE METHODS

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

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Regulation of single-cell genome organization into TADs and chromatin nanodomains

(2020) Quentin Szabo et al.   NATURE GENETICS

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

RNA polymerases as moving barriers to condensin loop extrusion

(2019) Hugo B. Brandão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells

(2019) Simona Bianco et al.   Cell Reports

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus 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

Challenges and guidelines toward 4D nucleome data and model standards

(2018) Marc A. Marti-Renom et al.   NATURE GENETICS

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

(2018) Adam Buckle et al.   MOLECULAR CELL

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

(2018) Bogdan Bintu et al.   SCIENCE

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

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

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

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

Structural insights of nucleosome and the 30-nm chromatin fiber

(2016) Ping Zhu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2016) Alistair N. Boettiger et al.   NATURE

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

(2016) Rafael D Acemel et al.   NATURE GENETICS

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

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

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Compaction and segregation of sister chromatids via active loop extrusion

(2016) Anton Goloborodko et al.   eLife

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

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

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

(2015) François Serra et al.   FEBS LETTERS

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

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

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti 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

Chromatin as dynamic 10-nm fibers

(2014) Kazuhiro Maeshima et al.   CHROMOSOMA

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

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

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

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

(2012) Tom Sexton et al.   CELL

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

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

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

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

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

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

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

(2010) Guillaume J. Filion et al.   CELL

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Living without 30nm chromatin fibers

(2010) Eden Fussner et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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