Genome folding and refolding in differentiation and cellular senescence

On the existence and functionality of topologically associating domains

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

Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control

(2020) Valentina Casa et al.   GENOME RESEARCH

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

Parental-to-embryo switch of chromosome organization in early embryogenesis

(2020) Samuel Collombet et al.   NATURE

3D ATAC-PALM: super-resolution imaging of the accessible genome

(2020) Liangqi Xie et al.   NATURE METHODS

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase

(2019) Lucas Patel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

L1 drives IFN in senescent cells and promotes age-associated inflammation

(2019) Marco De Cecco 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

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

Nuclear pore density controls heterochromatin reorganization during senescence

(2019) Charlene Boumendil et al.   GENES & DEVELOPMENT

Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains

(2019) Kelvin See et al.   DEVELOPMENT

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

(2019) Joke G. van Bemmel et al.   NATURE GENETICS

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

(2019) Josef Redolfi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States

(2019) Stephanie L. Battle et al.   Stem Cell Reports

iHi-C 2.0: A simple approach for mapping native spatial chromatin organisation from low cell numbers

(2019) Athanasia Mizi et al.   METHODS

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

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

(2019) Alessandra Dall’Agnese 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

Polymer Modeling Predicts Chromosome Reorganization in Senescence

(2019) Michael Chiang et al.   Cell Reports

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos

(2019) Zhenhai Du et al.   MOLECULAR CELL

Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization

(2019) Osamu Iwasaki et al.   Nature Communications

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

(2018) Sofia A. Quinodoz et al.   CELL

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

(2018) Gangqing Hu et al.   IMMUNITY

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

(2018) Anne Zirkel et al.   MOLECULAR CELL

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

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

(2018) James H. Sun et al.   CELL

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

(2018) Jiao Sima et al.   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

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

(2018) Aleksandra Pękowska et al.   Cell Systems

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

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

(2017) François Aymard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2017) Stefan Dillinger et al.   PLoS One

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

(2017) François Aymard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

(2016) Lilija Brant et al.   Molecular Systems Biology

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Reorganization of chromosome architecture in replicative cellular senescence

(2016) Steven W. Criscione et al.   Science Advances

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

(2015) Darío G. Lupiáñez et al.   CELL

Global Reorganization of the Nuclear Landscape in Senescent Cells

(2015) Tamir Chandra et al.   Cell Reports

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

(2014) Suhas S.P. Rao et al.   CELL

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Aging, Cellular Senescence, and Cancer

(2012) Judith Campisi   Annual Review of Physiology

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

(2012) Tamir Chandra et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Lessons from senescence: Chromatin maintenance in non-proliferating cells

(2011) Taranjit Singh Rai et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

HMGB proteins: Interactions with DNA and chromatin

(2010) Michal Štros   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Senescence impairs successful reprogramming to pluripotent stem cells

(2009) A. Banito et al.   GENES & DEVELOPMENT

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

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