Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes
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Title
Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes
Authors
Keywords
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Journal
Nature Communications
Volume 14, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2023-02-06
DOI
10.1038/s41467-023-36364-9
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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
- Annotation of chromatin states in 66 complete mouse epigenomes during development
- (2021) Arjan van der Velde et al. Communications Biology
- AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis
- (2021) Shaopeng Liu et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Derivation of trophoblast stem cells from naïve human pluripotent stem cells
- (2020) Chen Dong et al. eLife
- Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity
- (2020) Xiaotian Zhang et al. MOLECULAR CELL
- Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes
- (2020) Adam G. Diehl et al. Nature Communications
- Functional signatures of evolutionarily young CTCF binding sites
- (2020) Dhoyazan Azazi et al. BMC BIOLOGY
- Cell-type-specific 3D epigenomes in the developing human cortex
- (2020) Michael Song et al. NATURE
- The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads
- (2019) Yang Liao et al. NUCLEIC ACIDS RESEARCH
- EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains
- (2019) Maria C. Donaldson-Collier et al. NATURE GENETICS
- WashU Epigenome Browser update 2019
- (2019) Daofeng Li et al. NUCLEIC ACIDS RESEARCH
- Developmentally regulated Shh expression is robust to TAD perturbations
- (2019) Iain Williamson et al. DEVELOPMENT
- Key role for CTCF in establishing chromatin structure in human embryos
- (2019) Xuepeng Chen et al. NATURE
- CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens
- (2018) Jean-Paul Concordet et al. NUCLEIC ACIDS RESEARCH
- Hormone-control regions mediate steroid receptor–dependent genome organization
- (2018) François Le Dily et al. GENOME RESEARCH
- Trans-ethnic association study of blood pressure determinants in over 750,000 individuals
- (2018) Ayush Giri et al. NATURE GENETICS
- The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes
- (2017) Hui Fan et al. GENOME RESEARCH
- Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
- (2017) Douglas H. Phanstiel et al. MOLECULAR CELL
- The 4D nucleome project
- (2017) Job Dekker et al. NATURE
- Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
- (2017) Maxwell R Mumbach et al. NATURE GENETICS
- Chromatin-state discovery and genome annotation with ChromHMM
- (2017) Jason Ernst et al. Nature Protocols
- The Encyclopedia of DNA elements (ENCODE): data portal update
- (2017) Carrie A Davis et al. NUCLEIC ACIDS RESEARCH
- Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus
- (2017) Vasavi Sundaram et al. Nature Communications
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
- (2017) Simon Fishilevich et al. Database-The Journal of Biological Databases and Curation
- Structural organization of the inactive X chromosome in the mouse
- (2016) Luca Giorgetti et al. NATURE
- HiChIP: efficient and sensitive analysis of protein-directed genome architecture
- (2016) Maxwell R Mumbach et al. NATURE METHODS
- Regulatory activities of transposable elements: from conflicts to benefits
- (2016) Edward B. Chuong et al. NATURE REVIEWS GENETICS
- Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture
- (2016) Emily M. Darrow et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
- (2016) Anthony D. Schmitt 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
- Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
- (2016) Neva C. Durand et al. Cell Systems
- CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
- (2015) Miguel A Moreno-Mateos et al. NATURE METHODS
- Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
- (2015) Matteo Vietri Rudan et al. Cell Reports
- Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements
- (2015) Christopher E Ellison et al. eLife
- HTSeq--a Python framework to work with high-throughput sequencing data
- (2014) S. Anders et al. BIOINFORMATICS
- Widespread contribution of transposable elements to the innovation of gene regulatory networks
- (2014) Vasavi Sundaram et al. GENOME RESEARCH
- Lineage-specific compaction ofTcrbrequires a chromatin barrier to protect the function of a long-range tethering element
- (2014) Kinjal Majumder et al. JOURNAL OF EXPERIMENTAL MEDICINE
- Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins
- (2014) Gurkan Guntas et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
- (2013) Pierre-Étienne Jacques et al. PLoS Genetics
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
- (2012) Iouri Chepelev et al. CELL RESEARCH
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon 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
- Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome
- (2012) Xiaochun Ni et al. PLOS BIOLOGY
- Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
- (2011) Vincent J Lynch et al. NATURE GENETICS
- Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
- (2011) A. P. Jason de Koning et al. PLoS Genetics
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
- (2010) Galih Kunarso et al. NATURE GENETICS
- 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
- Evolution of the mammalian transcription factor binding repertoire via transposable elements
- (2008) G. Bourque et al. GENOME RESEARCH
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