Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
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Title
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
Authors
Keywords
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Journal
eLife
Volume 7, Issue -, Pages -
Publisher
eLife Sciences Organisation, Ltd.
Online
2018-04-12
DOI
10.7554/elife.33084
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Related references
Note: Only part of the references are listed.- Transposable elements are the primary source of novelty in primate gene regulation
- (2017) Marco Trizzino et al. GENOME RESEARCH
- Heritable L1 retrotransposition in the mouse primordial germline and early embryo
- (2017) Sandra R. Richardson et al. GENOME RESEARCH
- Impact of regulatory variation across human iPSCs and differentiated cells
- (2017) Nicholas E. Banovich et al. GENOME RESEARCH
- Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints
- (2017) Corinne N. Simonti et al. MOLECULAR BIOLOGY AND EVOLUTION
- KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
- (2017) Michaël Imbeault et al. NATURE
- Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus
- (2017) Vasavi Sundaram et al. Nature Communications
- TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells
- (2017) Per Ludvik Brattås et al. Cell Reports
- Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues
- (2016) Gabriela Ecco et al. DEVELOPMENTAL CELL
- CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome
- (2016) Jonathan Göke et al. EMBO REPORTS
- Multiparameter functional diversity of human C2H2 zinc finger proteins
- (2016) Frank W. Schmitges et al. GENOME RESEARCH
- Regulatory activities of transposable elements: from conflicts to benefits
- (2016) Edward B. Chuong et al. NATURE REVIEWS GENETICS
- 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
- The DNA methyltransferase DNMT3C protects male germ cells from transposon activity
- (2016) Joan Barau et al. SCIENCE
- Regulatory evolution of innate immunity through co-option of endogenous retroviruses
- (2016) E. B. Chuong et al. SCIENCE
- Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells
- (2016) Sabine Klawitter et al. Nature Communications
- Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs
- (2016) Courtney K. Burrows et al. PLoS Genetics
- An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells
- (2016) Marius Walter et al. eLife
- Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest
- (2015) Sara L. Prescott et al. CELL
- The evolution of gene expression and binding specificity of the largest transcription factor family in primates
- (2015) Adamandia Kapopoulou et al. EVOLUTION
- Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
- (2015) Edward J. Grow et al. NATURE
- Integrative analysis of 111 reference human epigenomes
- (2015) Anshul Kundaje et al. NATURE
- C2H2 zinc finger proteins greatly expand the human regulatory lexicon
- (2015) Hamed S Najafabadi et al. NATURE BIOTECHNOLOGY
- Sound of silence: the properties and functions of repressive Lys methyltransferases
- (2015) Chiara Mozzetta et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- The UCSC Genome Browser database: 2016 update
- (2015) Matthew L. Speir et al. NUCLEIC ACIDS RESEARCH
- Retrotransposons shape species-specific embryonic stem cell gene expression
- (2015) Luisa Robbez-Masson et al. Retrovirology
- Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy
- (2015) Vincent J. Lynch et al. Cell Reports
- A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
- (2015) Irene Gallego Romero et al. eLife
- HTSeq--a Python framework to work with high-throughput sequencing data
- (2014) S. Anders et al. BIOINFORMATICS
- Evolutionally dynamic L1 regulation in embryonic stem cells
- (2014) N. Castro-Diaz et al. GENES & DEVELOPMENT
- Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency
- (2014) Marc Friedli et al. GENOME RESEARCH
- Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements
- (2014) Priscilla Turelli et al. GENOME RESEARCH
- Retroviral Transcriptional Regulation and Embryonic Stem Cells: War and Peace
- (2014) Sharon Schlesinger et al. MOLECULAR AND CELLULAR BIOLOGY
- An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
- (2014) Frank M. J. Jacobs et al. NATURE
- Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
- (2014) Jichang Wang et al. NATURE
- DNA methylation dynamics of the human preimplantation embryo
- (2014) Zachary D. Smith et al. NATURE
- Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance
- (2014) Alexandre Fort et al. NATURE GENETICS
- The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
- (2014) Xinyi Lu et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Chimpanzee-Specific Endogenous Retrovirus Generates Genomic Variations in the Chimpanzee Genome
- (2014) Seyoung Mun et al. PLoS One
- Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes
- (2014) Petra C Schwalie et al. GENOME BIOLOGY
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts
- (2014) Charity W Law et al. GENOME BIOLOGY
- featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
- (2013) Y. Liao et al. BIOINFORMATICS
- De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET
- (2013) H. M. Rowe et al. DEVELOPMENT
- Differential L1 regulation in pluripotent stem cells of humans and apes
- (2013) Maria C. N. Marchetto et al. NATURE
- DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
- (2013) Mingchao Xie et al. NATURE GENETICS
- Endogenous retroviruses function as species-specific enhancer elements in the placenta
- (2013) Edward B Chuong et al. NATURE GENETICS
- Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells
- (2013) Nina V Fuchs et al. Retrovirology
- The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
- (2013) Pierre-Étienne Jacques et al. PLoS Genetics
- Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
- (2013) Aurélie Kapusta 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
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Latent Regulatory Potential of Human-Specific Repetitive Elements
- (2012) Michelle C. Ward et al. MOLECULAR CELL
- Embryonic stem cell potency fluctuates with endogenous retrovirus activity
- (2012) Todd S. Macfarlan et al. NATURE
- ENCODE Data in the UCSC Genome Browser: year 5 update
- (2012) Kate R. Rosenbloom et al. NUCLEIC ACIDS RESEARCH
- Fast Computation and Applications of Genome Mappability
- (2012) Thomas Derrien et al. PLoS One
- HIV infection and HERV expression: a review
- (2012) Antoinette C van der Kuyl Retrovirology
- HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency
- (2012) Federico A Santoni et al. Retrovirology
- The KRAB-ZFP/KAP1 System Contributes to the Early Embryonic Establishment of Site-Specific DNA Methylation Patterns Maintained during Development
- (2012) Simon Quenneville et al. Cell Reports
- Transposable elements reveal a stem cell-specific class of long noncoding RNAs
- (2012) David Kelley et al. GENOME BIOLOGY
- DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs
- (2011) Mohammad M. Karimi et al. Cell Stem Cell
- Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification
- (2011) C. E. Cain et al. GENETICS
- Coevolution of retroelements and tandem zinc finger genes
- (2011) J. H. Thomas et al. GENOME RESEARCH
- Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility
- (2011) Silke Wissing et al. HUMAN MOLECULAR GENETICS
- Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
- (2011) Vincent J Lynch et al. NATURE GENETICS
- A bioinformatic assay for pluripotency in human cells
- (2011) Franz-Josef Müller et al. NATURE METHODS
- Dynamic control of endogenous retroviruses during development
- (2011) Helen M. Rowe et al. VIROLOGY
- Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
- (2011) A. P. Jason de Koning et al. PLoS Genetics
- Polycomb complexes act redundantly to repress genomic repeats and genes
- (2010) M. Leeb et al. GENES & DEVELOPMENT
- KAP1 controls endogenous retroviruses in embryonic stem cells
- (2010) Helen M. Rowe et al. NATURE
- Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
- (2010) Toshiyuki Matsui et al. NATURE
- Discovery and characterization of chromatin states for systematic annotation of the human genome
- (2010) Jason Ernst et al. NATURE BIOTECHNOLOGY
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
- (2010) Galih Kunarso et al. NATURE GENETICS
- Estimating enrichment of repetitive elements from high-throughput sequence data
- (2010) Daniel S Day et al. GENOME 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
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state
- (2009) S. Bilodeau et al. GENES & DEVELOPMENT
- Sex-specific and lineage-specific alternative splicing in primates
- (2009) R. Blekhman et al. GENOME RESEARCH
- ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions
- (2009) Dominic Schmidt et al. METHODS
- Embryonic stem cells use ZFP809 to silence retroviral DNAs
- (2009) Daniel Wolf et al. NATURE
- The regulated retrotransposon transcriptome of mammalian cells
- (2009) Geoffrey J Faulkner et al. NATURE GENETICS
- The impact of retrotransposons on human genome evolution
- (2009) Richard Cordaux et al. NATURE REVIEWS GENETICS
- 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
- Species-Specific Transcription in Mice Carrying Human Chromosome 21
- (2008) M. D. Wilson et al. SCIENCE
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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