Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

(2021) Elizabeth Ing-Simmons et al.   NATURE GENETICS

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M

(2020) Andrés M. Cardozo Gizzi et al.   Nature Protocols

Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping

(2020) V. Loubiere et al.   Science Advances

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

The emergence of genome architecture and zygotic genome activation

(2020) Antoine Vallot et al.   CURRENT OPINION IN CELL BIOLOGY

Enhancer-promoter communication: hubs or loops?

(2020) Bomyi Lim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Positive and Negative Control of Enhancer-Promoter Interactions by Other DNA Loops Generates Specificity and Tunability

(2019) Nan Hao et al.   Cell Reports

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

(2019) Leslie J. Mateo et al.   NATURE

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

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Preformed chromatin topology assists transcriptional robustness of Shh during limb development

(2019) Christina Paliou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-enhancer transcriptional hubs confer phenotypic robustness

(2019) Albert Tsai et al.   eLife

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts

(2019) Stephen S. Gisselbrecht et al.   MOLECULAR CELL

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

(2019) A. Marieke Oudelaar et al.   Nature Communications

Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression

(2019) Annick Lesne et al.   Genes

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

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

(2018) Bo Gu et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies

(2018) Marie-Odile Baudement et al.   GENOME RESEARCH

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

(2018) Caroline R. Bartman et al.   MOLECULAR CELL

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

(2018) A. Marieke Oudelaar et al.   NATURE GENETICS

Mechanisms regulating zygotic genome activation

(2018) Katharine N. Schulz et al.   NATURE REVIEWS GENETICS

REDfly: the transcriptional regulatory element database for Drosophila

(2018) John Rivera et al.   NUCLEIC ACIDS RESEARCH

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

(2018) Jeremy Dufourt et al.   Nature Communications

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

(2018) Mustafa Mir et al.   eLife

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

(2017) Adam J Rubin et al.   NATURE GENETICS

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map

(2017) Kyle P. Eagen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

(2017) Stefanie L. Morgan et al.   Nature Communications

A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster

(2017) Danielle C. Hamm et al.   PLoS Genetics

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

Concentration dependent chromatin states induced by the bicoid morphogen gradient

(2017) Colleen E Hannon et al.   eLife

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

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

(2016) Alistair N. Boettiger et al.   NATURE

Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo

(2016) Lisa Deignan et al.   PLoS Genetics

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

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

(2015) Suhas S.P. Rao et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CTCF-dependent co-localization of canonical Smad signaling factors at architectural protein binding sites inD. melanogaster

(2015) Kevin Van Bortle et al.   CELL CYCLE

Zelda overcomes the high intrinsic nucleosome barrier at enhancers duringDrosophilazygotic genome activation

(2015) Yujia Sun et al.   GENOME RESEARCH

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the earlyDrosophilaembryo

(2015) Katharine N. Schulz et al.   GENOME RESEARCH

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains

(2014) Wibke Schwarzer et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

Maternal control of the Drosophila dorsal-ventral body axis

(2014) David S. Stein et al.   Wiley Interdisciplinary Reviews-Developmental Biology

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha et al.   CELL

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

(2013) A. Saunders et al.   GENES & DEVELOPMENT

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

(2013) Kai Chen et al.   eLife

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

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Transcriptional repression via antilooping in the Drosophila embryo

(2012) V. S. Chopra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

The Bicoid Morphogen System

(2010) Aude Porcher et al.   CURRENT BIOLOGY

A conserved activation element in BMP signaling during Drosophila development

(2009) Alexander Weiss et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

cis-Regulatory networks during development: a view of Drosophila

(2008) Stefan Bonn et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE