Visualizing DNA folding and RNA in embryos at single-cell resolution

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

(2019) Andrés M. Cardozo Gizzi et al.   MOLECULAR CELL

The Insulator Protein CTCF Is Required for CorrectHoxGene Expression, but Not for Embryonic Development inDrosophila

(2018) Maria Cristina Gambetta et al.   GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

The Insulator Protein CTCF Is Required for CorrectHoxGene Expression, but Not for Embryonic Development inDrosophila

(2018) Maria Cristina Gambetta et al.   GENETICS

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

(2018) Quentin Szabo et al.   Science Advances

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

(2018) Bjørt K. Kragesteen et al.   NATURE GENETICS

Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis

(2018) Thierry Cheutin et al.   Nature Communications

Organizational principles of 3D genome architecture

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

REDfly: the transcriptional regulatory element database for Drosophila

(2018) John Rivera et al.   NUCLEIC ACIDS RESEARCH

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

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

(2017) Sharmistha Kundu et al.   MOLECULAR CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

CTCF-mediated topological boundaries during development foster appropriate gene regulation

(2016) Varun Narendra et al.   GENES & DEVELOPMENT

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

(2016) Alistair N. Boettiger et al.   NATURE

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

The open for business model of the bithorax complex in Drosophila

(2015) Robert K. Maeda et al.   CHROMOSOMA

The boundary paradox in the Bithorax complex

(2015) Olga Kyrchanova et al.   MECHANISMS OF DEVELOPMENT

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Impaired climbing and flight behaviour in Drosophila melanogaster following carbon dioxide anaesthesia

(2015) Nathan R. Bartholomew et al.   Scientific Reports

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine 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

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

Cooperativity, Specificity, and Evolutionary Stability of Polycomb Targeting in Drosophila

(2014) Bernd Schuettengruber et al.   Cell Reports

H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex

(2014) Sarah K Bowman et al.   eLife

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

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

The Border Between the Ultrabithorax and abdominal-A Regulatory Domains in the Drosophila Bithorax Complex

(2013) W. Bender et al.   GENETICS

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

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

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Ring1B Compacts Chromatin Structure and Represses Gene Expression Independent of Histone Ubiquitination

(2010) Ragnhild Eskeland et al.   MOLECULAR CELL

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS