Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

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

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

Loop competition and extrusion model predicts CTCF interaction specificity

(2021) Wang Xi et al.   Nature Communications

Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

(2021) Jing Luan et al.   Cell Reports

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

(2021) Hui Huang et al.   NATURE GENETICS

Deletion of CTCF sites in the SHH locus alters enhancer–promoter interactions and leads to acheiropodia

(2021) Aki Ushiki et al.   Nature Communications

Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations

(2021) Christopher Chase Bolt et al.   Nature Communications

Induction of a chromatin boundary in vivo upon insertion of a TAD border

(2021) Andréa Willemin et al.   PLoS Genetics

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

(2020) Elena M. Pugacheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of CTCF binding to transcriptional activity at the HOXA locus in NPM1-mutant AML cells

(2020) Reza Ghasemi et al.   LEUKEMIA

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

(2020) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

A complex regulatory landscape involved in the development of mammalian external genitals

(2020) Ana Rita Amândio et al.   eLife

pyGenomeTracks: reproducible plots for multivariate genomic data sets

(2020) Lucille Lopez-Delisle et al.   BIOINFORMATICS

Cohesin subunit RAD21: From biology to disease

(2020) Haizi Cheng et al.   GENE

Mammalian-specific ectodermal enhancers control the expression ofHoxcgenes in developing nails and hair follicles

(2020) Marc Fernandez-Guerrero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin topology and the timing of enhancer function at theHoxDlocus

(2020) Eddie Rodríguez-Carballo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

Loop formation by SMC complexes: turning heads, bending elbows, and fixed anchors

(2019) Ángela Sedeño Cacciatore et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

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

(2019) Alexandra Despang 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

The constrained architecture of mammalian Hox gene clusters

(2019) Fabrice Darbellay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Defining Functionally Relevant Spatial Chromatin Domains: It is a TAD Complicated

(2019) Natalia Sikorska et al.   JOURNAL OF MOLECULAR BIOLOGY

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Fidel Ramírez et al.   Nature Communications

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development

(2018) Nayuta Yakushiji-Kaminatsui et al.   PLOS BIOLOGY

Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

(2017) Jacqueline Deschamps et al.   GENES & DEVELOPMENT

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

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

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

(2017) Hideharu Hashimoto et al.   MOLECULAR CELL

CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

(2017) Gang Ren et al.   MOLECULAR CELL

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

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

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

A role for HOX13 proteins in the regulatory switch between TADs at theHoxDlocus

(2016) Leonardo Beccari et al.   GENES & DEVELOPMENT

CTCF-mediated topological boundaries during development foster appropriate gene regulation

(2016) Varun Narendra et al.   GENES & DEVELOPMENT

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster

(2016) Yu-Cheng Tsai et al.   NUCLEIC ACIDS RESEARCH

Co-regulation of paralog genes in the three-dimensional chromatin architecture

(2016) Jonas Ibn-Salem et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Control ofHoxdgene transcription in the mammary bud by hijacking a preexisting regulatory landscape

(2016) Ruben Schep et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

(2016) Johannes Stigler et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

(2016) Isabel Guerreiro et al.   eLife

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

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

(2015) Carlos Gómez-Marín 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

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

The Role of CCCTC-Binding Factor (CTCF) in Genomic Imprinting, Development, and Reproduction1

(2014) Maurício M. Franco et al.   BIOLOGY OF REPRODUCTION

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

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

Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus

(2014) N. Gosalia et al.   NUCLEIC ACIDS RESEARCH

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

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

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

Duplications of hox gene clusters and the emergence of vertebrates

(2013) Natalia Soshnikova et al.   DEVELOPMENTAL BIOLOGY

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

(2013) G. Andrey et al.   SCIENCE

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

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

Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters

(2012) P. Tschopp et al.   DEVELOPMENT

CTCF: insights into insulator function during development

(2012) M. Herold et al.   DEVELOPMENT

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization

(2012) Jesse D. Ziebarth et al.   NUCLEIC ACIDS RESEARCH

CTCF/cohesin-mediated DNA looping is required for protocadherin   promoter choice

(2012) Y. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

CTCF-binding elements mediate control of V(D)J recombination

(2011) Chunguang Guo et al.   NATURE

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Hox genes and regional patterning of the vertebrate body plan

(2010) Moises Mallo et al.   DEVELOPMENTAL BIOLOGY

Functional Analysis of CTCF During Mammalian Limb Development

(2010) Natalia Soshnikova et al.   DEVELOPMENTAL CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Axial patterning in snakes and caecilians: Evidence for an alternative interpretation of the Hox code

(2009) Joost M. Woltering et al.   DEVELOPMENTAL BIOLOGY

Cdx and Hox Genes Differentially Regulate Posterior Axial Growth in Mammalian Embryos

(2009) Teddy Young et al.   DEVELOPMENTAL CELL

Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development

(2008) L.-B. Wan et al.   DEVELOPMENT