Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

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

(2018) Sofia A. Quinodoz et al.   CELL

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Computational 3D genome modeling using Chrom3D

(2018) Jonas Paulsen et al.   Nature Protocols

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

(2018) Quentin Szabo et al.   Science Advances

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

Coaching from the sidelines: the nuclear periphery in genome regulation

(2018) Abigail Buchwalter et al.   NATURE REVIEWS GENETICS

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

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

(2018) Bogdan Bintu et al.   SCIENCE

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

(2017) Michael I. Robson et al.   GENOME RESEARCH

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

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

(2017) Takashi Nagano et al.   NATURE

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions

(2017) Henri Niskanen et al.   NUCLEIC ACIDS RESEARCH

Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability

(2017) Anna C. Salzberg et al.   PLoS One

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks

(2016) Pedro Olivares-Chauvet et al.   NATURE

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

(2016) Alistair N. Boettiger et al.   NATURE

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

On TADs and LADs: Spatial Control Over Gene Expression

(2016) Adriana Gonzalez-Sandoval et al.   TRENDS IN GENETICS

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments

(2015) Thomas Cremer et al.   FEBS LETTERS

Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B

(2015) Torunn Rønningen et al.   GENOME RESEARCH

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

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje 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

A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules

(2015) Akshay Shah et al.   BMC GENOMICS

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

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

(2014) Suhas S.P. Rao et al.   CELL

A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

(2014) Jonas Paulsen et al.   NUCLEIC ACIDS RESEARCH

Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

(2014) Eivind Lund et al.   NUCLEIC ACIDS RESEARCH

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

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

The Genomic HyperBrowser: an analysis web server for genome-scale data

(2013) Geir K. Sandve et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Jon-Matthew Belton et al.   METHODS

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

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells

(2012) Jean-Luc Boulland et al.   STEM CELLS AND DEVELOPMENT

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

(2009) Bo Wen et al.   NATURE GENETICS

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY