CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles

Genome organization controls transcriptional dynamics during development

(2022) Philippe J. Batut et al.   SCIENCE

Regulating specificity in enhancer–promoter communication

(2022) Charalampos Chrysovalantis Galouzis et al.   CURRENT OPINION IN CELL BIOLOGY

The role of insulators and transcription in 3D chromatin organization of flies

(2022) Keerthi T. Chathoth et al.   GENOME RESEARCH

Essential role of Cp190 in physical and regulatory boundary formation

(2022) Anjali Kaushal et al.   Science Advances

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

(2022) Chiara Anania et al.   NATURE GENETICS

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

(2021) Naoki Kubo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

(2021) Anjali Kaushal et al.   Nature Communications

Chromatin architecture transitions from zebrafish sperm through early embryogenesis

(2021) Candice L. Wike et al.   GENOME RESEARCH

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

(2021) Sergio Martin Espinola et al.   NATURE GENETICS

M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity

(2021) Indira Bag et al.   Nature Communications

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

Efficient low-cost chromatin profiling with CUT&Tag

(2020) Hatice S. Kaya-Okur et al.   Nature Protocols

Computer vision for pattern detection in chromosome contact maps

(2020) Cyril Matthey-Doret et al.   Nature Communications

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

Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome

(2019) Keerthi T. Chathoth et al.   GENOME RESEARCH

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

Chromatin Architecture in the Fly: Living without CTCF/Cohesin Loop Extrusion?

(2019) Nicholas E. Matthews et al.   BIOESSAYS

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

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

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

The Role of Insulation in Patterning Gene Expression

(2019) Özdemir et al.   Genes

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

(2018) Maria Cristina Gambetta et al.   GENETICS

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

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

(2018) Qi Wang et al.   Nature Communications

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

(2018) Maria Cristina Gambetta et al.   GENETICS

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

(2018) Ignacio E. Schor et al.   CURRENT BIOLOGY

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

(2018) Bogdan Bintu et al.   SCIENCE

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

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

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

(2017) Sherif El-Sharnouby et al.   PLoS One

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Zygotic Genome Activation Triggers the DNA Replication Checkpoint at the Midblastula Transition

(2015) Shelby A. Blythe et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

(2015) Rodrigo Peña-Hernández et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function

(2014) S. Cuartero et al.   EMBO JOURNAL

Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair inDrosophila

(2014) Scott J. Gratz et al.   GENETICS

Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

(2014) Oksana Maksimenko et al.   GENOME RESEARCH

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome

(2014) Jutta Vogelmann et al.   PLoS Genetics

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

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

The insulator protein Suppressor of Hairy-wing is an essential transcriptional repressor in the Drosophila ovary

(2013) A. A. Soshnev et al.   DEVELOPMENT

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins

(2013) Jingping Yang et al.   Nature Communications

The Drosophila eve Insulator Homie Promotes eve Expression and Protects the Adjacent Gene from Repression by Polycomb Spreading

(2013) Miki Fujioka et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Tom Sexton et al.   CELL

Depleting Gene Activities in Early Drosophila Embryos with the "Maternal-Gal4-shRNA" System

(2012) M. V. Staller et al.   GENETICS

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

(2012) K. Van Bortle et al.   GENOME RESEARCH

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

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

(2012) Stefan Bonn et al.   Nature Protocols

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

Active promoters and insulators are marked by the centrosomal protein 190

(2009) Marek Bartkuhn et al.   EMBO JOURNAL

Stalled Hox promoters as chromosomal boundaries

(2009) V. S. Chopra et al.   GENES & DEVELOPMENT

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

(2009) N. Jiang et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2008) Hsiao-Lan Liang et al.   NATURE