C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization

3D genome architecture from populations to single cells

(2015) Mayra Furlan-Magaril et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Spatial re-organization of myogenic regulatory sequences temporally controls gene expression

(2015) Akihito Harada et al.   NUCLEIC ACIDS RESEARCH

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

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

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

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

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

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C

(2014) Nicola H. Dryden et al.   GENOME RESEARCH

Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization

(2014) Minna U. Kaikkonen et al.   NUCLEIC ACIDS RESEARCH

Classifying leukemia types with chromatin conformation data

(2014) Mathieu Rousseau et al.   GENOME BIOLOGY

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

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

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

Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

(2013) Zong Wei et al.   Cell Stem Cell

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

(2013) V. C. Seitan et al.   GENOME RESEARCH

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

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Genomic Interaction Profiles in Breast Cancer Reveal Altered Chromatin Architecture

(2013) Michael J. Zeitz et al.   PLoS One

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

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

(2012) Yu Zhang et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

A decade of 3C technologies: insights into nuclear organization

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

Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome

(2012) R. P. McCord et al.   GENOME RESEARCH

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

From cells to chromatin: Capturing snapshots of genome organization with 5C technology

(2012) Maria A. Ferraiuolo et al.   METHODS

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

(2012) Natalia Naumova et al.   METHODS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal 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

Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip

(2012) Tom Sexton et al.   Nature Protocols

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

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

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

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

Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations

(2008) V. K. Tiwari et al.   GENOME RESEARCH