CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression
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Title
CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression
Authors
Keywords
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Journal
Nature Communications
Volume 12, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-09-13
DOI
10.1038/s41467-021-25604-5
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Note: Only part of the references are listed.- Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
- (2021) Naoki Kubo et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Chromatin architecture transitions from zebrafish sperm through early embryogenesis
- (2021) Candice L. Wike et al. GENOME RESEARCH
- Three-dimensional folding dynamics of the Xenopus tropicalis genome
- (2021) Longjian Niu 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
- Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains
- (2020) Amanda Khoury et al. Nature Communications
- ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL
- (2020) Gordana Wutz et al. eLife
- CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response
- (2020) Grégoire Stik et al. NATURE GENETICS
- A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase
- (2020) Janne Purhonen et al. NUCLEIC ACIDS RESEARCH
- Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers
- (2020) Michiel J. Thiecke et al. Cell Reports
- Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish
- (2020) Yuvia A. Pérez-Rico et al. iScience
- ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
- (2020) Mette Bentsen et al. Nature Communications
- Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs
- (2019) Magdalena Laugsch et al. Cell Stem Cell
- Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- (2019) Charles E. Vejnar et al. GENOME RESEARCH
- 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
- 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
- Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification
- (2019) José M. Santos-Pereira et al. Nature Communications
- Developmentally regulated Shh expression is robust to TAD perturbations
- (2019) Iain Williamson et al. DEVELOPMENT
- Identification of significant chromatin contacts from HiChIP data by FitHiChIP
- (2019) Sourya Bhattacharyya et al. Nature Communications
- Key role for CTCF in establishing chromatin structure in human embryos
- (2019) Xuepeng Chen et al. NATURE
- An evolutionary perspective of regulatory landscape dynamics in development and disease
- (2018) Martin Franke et al. CURRENT OPINION IN CELL BIOLOGY
- CTCF knockout reveals an essential role for this protein during the zebrafish development
- (2018) Francisco Carmona-Aldana et al. MECHANISMS OF DEVELOPMENT
- Structural variation in the 3D genome
- (2018) Malte Spielmann et al. NATURE REVIEWS GENETICS
- Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development
- (2018) Lucas J.T. Kaaij et al. Cell Reports
- 4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data
- (2018) Ibai Irastorza-Azcarate et al. PLoS Computational Biology
- Organizational principles of 3D genome architecture
- (2018) M. Jordan Rowley et al. NATURE REVIEWS GENETICS
- The UCSC Genome Browser database: 2019 update
- (2018) Maximilian Haeussler et al. NUCLEIC ACIDS RESEARCH
- Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
- (2017) François Serra et al. PLoS Computational Biology
- CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart
- (2017) Melisa Gomez-Velazquez et al. PLoS Genetics
- Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals
- (2017) Rafael D. Acemel et al. Wiley Interdisciplinary Reviews-Developmental Biology
- CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation
- (2016) Matthias Merkenschlager et al. Annual Review of Genomics and Human Genetics
- The 3D Genome as Moderator of Chromosomal Communication
- (2016) Job Dekker 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
- Chromatin Domains: The Unit of Chromosome Organization
- (2016) Jesse R. Dixon et al. MOLECULAR CELL
- Formation of new chromatin domains determines pathogenicity of genomic duplications
- (2016) Martin Franke et al. NATURE
- UMI-4C for quantitative and targeted chromosomal contact profiling
- (2016) Omer Schwartzman et al. NATURE METHODS
- HiChIP: efficient and sensitive analysis of protein-directed genome architecture
- (2016) Maxwell R Mumbach et al. NATURE METHODS
- Organization and function of the 3D genome
- (2016) Boyan Bonev et al. NATURE REVIEWS GENETICS
- deepTools2: a next generation web server for deep-sequencing data analysis
- (2016) Fidel Ramírez et al. NUCLEIC ACIDS RESEARCH
- Activation of proto-oncogenes by disruption of chromosome neighborhoods
- (2016) D. Hnisz et al. SCIENCE
- Formation of Chromosomal Domains by Loop Extrusion
- (2016) Geoffrey Fudenberg et al. Cell Reports
- Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
- (2016) Neva C. Durand et al. Cell Systems
- Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
- (2015) Darío G. Lupiáñez et al. CELL
- CTCF Binding Polarity Determines Chromatin Looping
- (2015) Elzo de Wit et al. MOLECULAR CELL
- Condensin-driven remodelling of X chromosome topology during dosage compensation
- (2015) Emily Crane et al. NATURE
- CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
- (2015) Miguel A Moreno-Mateos et al. NATURE METHODS
- ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors
- (2015) Christian Schmidl et al. NATURE METHODS
- 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
- HTSeq--a Python framework to work with high-throughput sequencing data
- (2014) S. Anders et al. BIOINFORMATICS
- 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
- Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
- (2013) Jennifer E. Phillips-Cremins et al. CELL
- Topology of mammalian developmental enhancers and their regulatory landscapes
- (2013) Wouter de Laat et al. NATURE
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
- (2013) Jason D Buenrostro et al. NATURE METHODS
- Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish
- (2013) Michael Hiller et al. NUCLEIC ACIDS RESEARCH
- A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs
- (2013) G. Andrey et al. SCIENCE
- Comparison of Stain-Free gels with traditional immunoblot loading control methodology
- (2012) Alex D. Colella et al. ANALYTICAL BIOCHEMISTRY
- 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
- Hoxd13 Contribution to the Evolution of Vertebrate Appendages
- (2012) Renata Freitas et al. DEVELOPMENTAL CELL
- A fast algorithm for matrix balancing
- (2012) P. A. Knight et al. IMA JOURNAL OF NUMERICAL ANALYSIS
- Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains
- (2012) Chunhui Hou et al. MOLECULAR 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
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Loss of Maternal CTCF Is Associated with Peri-Implantation Lethality of Ctcf Null Embryos
- (2012) James M. Moore et al. PLoS One
- The Human Epigenome Browser at Washington University
- (2011) Xin Zhou et al. NATURE METHODS
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Functional Analysis of CTCF During Mammalian Limb Development
- (2010) Natalia Soshnikova et al. DEVELOPMENTAL CELL
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
- (2010) Sven Heinz et al. MOLECULAR CELL
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- CTCF: Master Weaver of the Genome
- (2009) Jennifer E. Phillips et al. CELL
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- CTCF regulates cell cycle progression of αβ T cells in the thymus
- (2008) Helen Heath et al. EMBO JOURNAL
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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