Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains
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Title
Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains
Authors
Keywords
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Journal
Nature Communications
Volume 11, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2020-01-07
DOI
10.1038/s41467-019-13753-7
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Note: Only part of the references are listed.- A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus
- (2018) A. Rasim Barutcu et al. Nature Communications
- Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl
- (2017) Georg A. Busslinger et al. NATURE
- CTCF and cohesin regulate chromatin loop stability with distinct dynamics
- (2017) Anders S Hansen et al. eLife
- Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations
- (2016) Phillippa C. Taberlay et al. GENOME RESEARCH
- 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
- Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
- (2015) Maxwell W. Libbrecht et al. GENOME RESEARCH
- Chromatin architecture reorganization during stem cell differentiation
- (2015) Jesse R. Dixon et al. NATURE
- Insulator dysfunction and oncogene activation in IDH mutant gliomas
- (2015) William A. Flavahan et al. NATURE
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation
- (2015) Varun Narendra et al. SCIENCE
- Tissue-based map of the human proteome
- (2015) M. Uhlen et al. SCIENCE
- Role of DNA Methylation in Modulating Transcription Factor Occupancy
- (2015) Matthew T. Maurano et al. Cell Reports
- Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
- (2015) Matteo Vietri Rudan et al. Cell Reports
- NGSANE: a lightweight production informatics framework for high-throughput data analysis
- (2014) Fabian A. Buske et al. BIOINFORMATICS
- Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data
- (2014) Wenyuan Li et al. BIOINFORMATICS
- ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
- (2014) Li Shen et al. BMC GENOMICS
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
- (2014) Suhas S.P. Rao et al. CELL
- Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- (2014) Phillippa C. Taberlay et al. GENOME RESEARCH
- Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
- (2014) F. Ay et al. GENOME RESEARCH
- Exploring long-range genome interactions using the WashU Epigenome Browser
- (2013) Xin Zhou et al. NATURE METHODS
- Genome engineering using the CRISPR-Cas9 system
- (2013) F Ann Ran et al. Nature Protocols
- CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation
- (2013) R. N. Plasschaert et al. NUCLEIC ACIDS RESEARCH
- Molecular circuit involving KLK4 integrates androgen and mTOR signaling in prostate cancer
- (2013) Y. Jin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- Software for Computing and Annotating Genomic Ranges
- (2013) Michael Lawrence et al. PLoS Computational Biology
- Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling
- (2012) Saul A. Bert et al. CANCER CELL
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Widespread plasticity in CTCF occupancy linked to DNA methylation
- (2012) H. Wang et al. GENOME RESEARCH
- Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
- (2012) Caryn S. Ross-Innes et al. NATURE
- 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
- Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
- (2012) Hebing Chen et al. PLoS One
- PeakRanger: A cloud-enabled peak caller for ChIP-seq data
- (2011) Xin Feng et al. BMC BIOINFORMATICS
- Association of KLK3 (PSA) genetic variants with prostate cancer risk and PSA levels
- (2011) Kathryn L. Penney et al. CARCINOGENESIS
- CTCF-mediated functional chromatin interactome in pluripotent cells
- (2011) Lusy Handoko et al. NATURE GENETICS
- Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus
- (2011) Y. J. Kim et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A framework for oligonucleotide microarray preprocessing
- (2010) Benilton S. Carvalho et al. BIOINFORMATICS
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- A CTCF-independent role for cohesin in tissue-specific transcription
- (2010) D. Schmidt et al. GENOME RESEARCH
- 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
- Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
- (2010) Marcel W. Coolen et al. NATURE CELL BIOLOGY
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- CTCF: Master Weaver of the Genome
- (2009) Jennifer E. Phillips et al. CELL
- Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
- (2009) Steffen Durinck et al. Nature Protocols
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms
- (2008) Vania Parelho et al. CELL
- Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
- (2008) S. Cuddapah et al. GENOME RESEARCH
- The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions
- (2008) Parimal Majumder et al. JOURNAL OF EXPERIMENTAL MEDICINE
- CTCF physically links cohesin to chromatin
- (2008) E. D. Rubio et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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