Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
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Title
Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
Authors
Keywords
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Journal
eLife
Volume 7, Issue -, Pages -
Publisher
eLife Sciences Publications, Ltd
Online
2018-08-02
DOI
10.7554/elife.35989
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Note: Only part of the references are listed.- Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements
- (2018) Bo Gu et al. SCIENCE
- Enhancer redundancy provides phenotypic robustness in mammalian development
- (2018) Marco Osterwalder et al. NATURE
- Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos
- (2017) Xinyi Wang et al. GENOME RESEARCH
- Transposable elements are the primary source of novelty in primate gene regulation
- (2017) Marco Trizzino et al. GENOME RESEARCH
- Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions
- (2017) Alex D. Greenwood et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo
- (2017) Joanna W Jachowicz et al. NATURE GENETICS
- Capturing Human Naïve Pluripotency in the Embryo and in the Dish
- (2017) Ludovic Zimmerlin et al. STEM CELLS AND DEVELOPMENT
- Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein
- (2017) Yong Lei et al. Nature Communications
- HERV-K(HML-2), a seemingly silent subtenant - but still waters run deep
- (2016) Kirsten Hanke et al. APMIS
- Editing DNA Methylation in the Mammalian Genome
- (2016) X. Shawn Liu et al. CELL
- 3D Chromosome Regulatory Landscape of Human Pluripotent Cells
- (2016) Xiong Ji et al. Cell Stem Cell
- Molecular Criteria for Defining the Naive Human Pluripotent State
- (2016) Thorold W. Theunissen et al. Cell Stem Cell
- Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes
- (2016) Sakthi D. Moorthy et al. GENOME RESEARCH
- Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire
- (2016) Peter J. Thompson et al. MOLECULAR CELL
- Genetic dissection of the α-globin super-enhancer in vivo
- (2016) Deborah Hay et al. NATURE GENETICS
- Regulatory activities of transposable elements: from conflicts to benefits
- (2016) Edward B. Chuong et al. NATURE REVIEWS GENETICS
- deepTools2: a next generation web server for deep-sequencing data analysis
- (2016) Fidel Ramírez et al. NUCLEIC ACIDS RESEARCH
- Repurposing the CRISPR-Cas9 system for targeted DNA methylation
- (2016) Aleksandar Vojta et al. NUCLEIC ACIDS RESEARCH
- Discovery of unfixed endogenous retrovirus insertions in diverse human populations
- (2016) Julia Halo Wildschutte et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Regulatory evolution of innate immunity through co-option of endogenous retroviruses
- (2016) E. B. Chuong et al. SCIENCE
- Massive contribution of transposable elements to mammalian regulatory sequences
- (2016) Nirmala Arul Rayan et al. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
- H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes
- (2016) Justin S. Becker et al. TRENDS IN GENETICS
- Nucleosomes impede Cas9 access to DNA in vivo and in vitro
- (2016) Max A Horlbeck et al. eLife
- A CRISPR-based approach for targeted DNA demethylation
- (2016) Xingxing Xu et al. Cell Discovery
- The Developmental Control of Transposable Elements and the Evolution of Higher Species
- (2015) Marc Friedli et al. Annual Review of Cell and Developmental Biology
- Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest
- (2015) Sara L. Prescott et al. CELL
- Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
- (2015) Lauren R. Polstein et al. GENOME RESEARCH
- Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers
- (2015) Denes Hnisz et al. MOLECULAR CELL
- Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
- (2015) Edward J. Grow et al. NATURE
- Hallmarks of pluripotency
- (2015) Alejandro De Los Angeles et al. NATURE
- StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
- (2015) Mihaela Pertea et al. NATURE BIOTECHNOLOGY
- Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers
- (2015) Isaac B Hilton et al. NATURE BIOTECHNOLOGY
- Functional annotation of native enhancers with a Cas9–histone demethylase fusion
- (2015) Nicola A Kearns et al. NATURE METHODS
- HISAT: a fast spliced aligner with low memory requirements
- (2015) Daehwan Kim et al. NATURE METHODS
- Highly efficient Cas9-mediated transcriptional programming
- (2015) Alejandro Chavez et al. NATURE METHODS
- Endogenous Retroviruses in the Genomics Era
- (2015) Welkin E. Johnson Annual Review of Virology
- Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
- (2014) Hongshan Jiang et al. BMC BIOINFORMATICS
- Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
- (2014) Yasuhiro Takashima et al. CELL
- Widespread contribution of transposable elements to the innovation of gene regulatory networks
- (2014) Vasavi Sundaram et al. GENOME RESEARCH
- Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
- (2014) Jichang Wang et al. NATURE
- Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
- (2014) Xuebing Wu et al. NATURE BIOTECHNOLOGY
- Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
- (2014) Cem Kuscu et al. NATURE BIOTECHNOLOGY
- Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis
- (2013) George R. Young et al. BIOESSAYS
- featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
- (2013) Y. Liao et al. BIOINFORMATICS
- Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System
- (2013) Baohui Chen et al. CELL
- CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
- (2013) Luke A. Gilbert et al. CELL
- Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system
- (2013) Albert W Cheng et al. CELL RESEARCH
- Modification of Enhancer Chromatin: What, How, and Why?
- (2013) Eliezer Calo et al. MOLECULAR CELL
- Endogenous retroviruses function as species-specific enhancer elements in the placenta
- (2013) Edward B Chuong et al. NATURE GENETICS
- RNA-guided gene activation by CRISPR-Cas9–based transcription factors
- (2013) Pablo Perez-Pinera et al. NATURE METHODS
- Genome engineering using the CRISPR-Cas9 system
- (2013) F Ann Ran et al. Nature Protocols
- Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
- (2013) Liying Yan et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Human-Specific HERV-K Insertion Causes Genomic Variations in the Human Genome
- (2013) Wonseok Shin et al. PLoS One
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- (2013) Ophir Shalem et al. SCIENCE
- The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
- (2013) Pierre-Étienne Jacques et al. PLoS Genetics
- SNF5 Is an Essential Executor of Epigenetic Regulation during Differentiation
- (2013) Jueng Soo You et al. PLoS Genetics
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
- (2013) Daehwan Kim et al. GENOME BIOLOGY
- Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- (2012) J. Wang et al. GENOME RESEARCH
- Embryonic stem cell potency fluctuates with endogenous retrovirus activity
- (2012) Todd S. Macfarlan et al. NATURE
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- (2012) Robert E. Thurman et al. NATURE
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- (2012) Ben Langmead et al. NATURE METHODS
- Endogenous viruses: insights into viral evolution and impact on host biology
- (2012) Cédric Feschotte et al. NATURE REVIEWS GENETICS
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- Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses
- (2011) Ravi P Subramanian et al. Retrovirology
- 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
- KAP1 controls endogenous retroviruses in embryonic stem cells
- (2010) Helen M. Rowe et al. NATURE
- A unique chromatin signature uncovers early developmental enhancers in humans
- (2010) Alvaro Rada-Iglesias et al. NATURE
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
- (2010) Galih Kunarso et al. NATURE GENETICS
- SVA retrotransposons: Evolution and genetic instability
- (2010) Dustin C. Hancks et al. SEMINARS IN CANCER BIOLOGY
- Epigenetic histone modifications of human transposable elements: genome defense versus exaptation
- (2010) Ahsan Huda et al. Mobile DNA
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Evolution of the mammalian transcription factor binding repertoire via transposable elements
- (2008) G. Bourque et al. GENOME RESEARCH
- Transposable elements and the evolution of regulatory networks
- (2008) Cédric Feschotte NATURE REVIEWS GENETICS
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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