Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

The Hierarchy of the 3D Genome

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

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

Step-Wise Methylation of Histone H3K9 Positions Heterochromatin at the Nuclear Periphery

(2012) Benjamin D. Towbin et al.   CELL

SnapShot: Chromosome Conformation Capture

(2012) Ofir Hakim et al.   CELL

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

Higher-order chromatin structure: bridging physics and biology

(2012) Geoffrey Fudenberg et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Structure and Function in the Budding Yeast Nucleus

(2012) A. Taddei et al.   GENETICS

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

(2012) H. Tjong et al.   GENOME RESEARCH

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

(2012) Chunhui Hou et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman 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

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Expression-Dependent Folding of Interphase Chromatin

(2012) Hansjoerg Jerabek et al.   PLoS One

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

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Discovering genome regulation with 3C and 3C-related technologies

(2011) Sylvain D. Ethier et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

(2011) Shelagh Boyle et al.   CHROMOSOME RESEARCH

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Chromatin globules: a common motif of higher order chromosome structure?

(2011) Amartya Sanyal et al.   CURRENT OPINION IN CELL BIOLOGY

A view of nuclear Polycomb bodies

(2011) Vincenzo Pirrotta et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Enhancer and promoter interactions—long distance calls

(2011) Ivan Krivega et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

(2011) O. Hakim et al.   GENOME RESEARCH

A view of the chromatin landscape

(2011) Lindsy M. Rapkin et al.   MICRON

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

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

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

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

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Repulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation

(2011) Manfred Bohn et al.   PLoS One

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

(2011) Marc A. Marti-Renom et al.   PLoS Computational Biology

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

(2011) Bas Tolhuis et al.   PLoS Genetics

Looping Probabilities in Model Interphase Chromosomes

(2010) Angelo Rosa et al.   BIOPHYSICAL JOURNAL

Upregulation of c-MYC in cis through a Large Chromatin Loop Linked to a Cancer Risk-Associated Single-Nucleotide Polymorphism in Colorectal Cancer Cells

(2010) J. B. Wright et al.   MOLECULAR AND CELLULAR 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

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Genomics tools for unraveling chromosome architecture

(2010) Bas van Steensel et al.   NATURE BIOTECHNOLOGY

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

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

The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture

(2010) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation

(2010) Hideki Tanizawa et al.   NUCLEIC ACIDS RESEARCH

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene

(2010) Nele Gheldof et al.   NUCLEIC ACIDS RESEARCH

Stable Morphology, but Dynamic Internal Reorganisation, of Interphase Human Chromosomes in Living Cells

(2010) Iris Müller et al.   PLoS One

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

(2010) Manfred Bohn et al.   PLoS One

8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC

(2010) N. Ahmadiyeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Entropic organization of interphase chromosomes

(2009) Peter R. Cook et al.   JOURNAL OF CELL BIOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

My5C: web tools for chromosome conformation capture studies

(2009) Bryan R Lajoie et al.   NATURE METHODS

Spatially confined folding of chromatin in the interphase nucleus

(2009) J. Mateos-Langerak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus

(2009) C. J. Ott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Yeast Silent Mating Type Loci Form Heterochromatic Clusters through Silencer Protein-Dependent Long-Range Interactions

(2009) Adriana Miele et al.   PLoS Genetics

Chromatin conformation signatures of cellular differentiation

(2009) James Fraser et al.   GENOME BIOLOGY

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

(2008) Suchit Jhunjhunwala et al.   CELL

A Polymeric Protein Anchors the Chromosomal Origin/ParB Complex at a Bacterial Cell Pole

(2008) Grant R. Bowman et al.   CELL

A Self-Associating Protein Critical for Chromosome Attachment, Division, and Polar Organization in Caulobacter

(2008) Gitte Ebersbach et al.   CELL

Association between active genes occurs at nuclear speckles and is modulated by chromatin environment

(2008) Jill M. Brown et al.   JOURNAL OF CELL BIOLOGY

The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions

(2008) Parimal Majumder et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Long-range chromosomal interactions and gene regulation

(2008) Adriana Miele et al.   Molecular BioSystems

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

(2008) Lars Guelen et al.   NATURE

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology