Quantitative differences in TAD border strength underly the TAD hierarchy in Drosophila chromosomes

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

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

(2018) Quentin Szabo et al.   Science Advances

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

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

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

(2017) Xiao-Tao Wang et al.   NUCLEIC ACIDS RESEARCH

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

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

3D genomics imposes evolution of the domain model of eukaryotic genome organization

(2016) Sergey V. Razin et al.   CHROMOSOMA

Liquid-like behavior of chromatin

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

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

(2016) Tung BK Le et al.   EMBO JOURNAL

Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments

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

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Unraveling the mechanisms of chromatin fibril packaging

(2016) Alexey A. Gavrilov et al.   Nucleus

Unraveling the mechanisms of chromatin fibril packaging

(2016) Alexey A. Gavrilov et al.   Nucleus

Identification of hierarchical chromatin domains

(2015) Caleb Weinreb et al.   BIOINFORMATICS

Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

(2015) Kyle P. Eagen et al.   CELL

Architectural proteins, transcription, and the three-dimensional organization of the genome

(2015) Caelin Cubeñas-Potts et al.   FEBS LETTERS

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

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems Biology

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Nanoscale spatial organization of theHoxDgene cluster in distinct transcriptional states

(2015) Pierre J. Fabre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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 without the 30-nm fiber

(2014) Sergey V Razin et al.   Epigenetics

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

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

Genetic Organization of Interphase Chromosome Bands and Interbands in Drosophila melanogaster

(2014) Igor F. Zhimulev et al.   PLoS One

Ectopically tethered CP190 induces large-scale chromatin decondensation

(2014) Sajad H. Ahanger et al.   Scientific Reports

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

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

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

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

The Hierarchy of the 3D Genome

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

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

(2013) Takashi Nagano et al.   NATURE

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) T. B. K. Le et al.   SCIENCE

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

(2013) Soizik Berlivet et al.   PLoS Genetics

The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture

(2012) Yolanda Markaki et al.   BIOESSAYS

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

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

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

HP1c casts light on dark matter

(2011) So Hee Kwon et al.   CELL CYCLE

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

(2010) Guillaume J. Filion et al.   CELL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Active promoters and insulators are marked by the centrosomal protein 190

(2009) Marek Bartkuhn et al.   EMBO JOURNAL

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

(2009) N. Jiang et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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