Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints

No abstract is available for this paper.

• Publication year

  2017

• Venue

  Molecular biology and evolution

• Publication date

  2017-11-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/molbev/msx219PMID 28961735PMCID PMC5850124
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Integration site selection by retroviruses and transposable elements in eukaryotes

  2017cited by this paper
• Transposable elements are the primary source of novelty in primate gene regulation

  2017cited by this paper
• Transposable elements in the mammalian embryo: pioneers surviving through stealth and service

  2016cited by this paper
• Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire.

  2016cited by this paper
• Regulatory activities of transposable elements: from conflicts to benefits

  2016influential reference
• Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape

  2016influential reference
• Regulatory evolution of innate immunity through co-option of endogenous retroviruses

  2016cited by this paper
• Origin and evolution of developmental enhancers in the mammalian neocortex

  2016influential reference
• Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer.

  2016cited by this paper
• A family of transposable elements co-opted into developmental enhancers in the mouse neocortex

  2015influential reference
• Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

  2015cited by this paper
• MIR retrotransposon sequences provide insulators to the human genome

  2015cited by this paper
• Integrative analysis of 111 reference human epigenomes

  2015cited by this paper
• Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

  2015cited by this paper
• Detecting Endogenous Retrovirus-Driven Tissue-Specific Gene Transcription

  2015cited by this paper
• Enhancer Evolution across 20 Mammalian Species

  2015influential reference
• JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

  2015cited by this paper
• Noncoding origins of anthropoid traits and a new null model of transposon functionalization

  2014cited by this paper
• An atlas of active enhancers across human cell types and tissues

  2014influential reference
• Widespread contribution of transposable elements to the innovation of gene regulatory networks

  2014influential reference
• The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

  2013cited by this paper
• Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

  2013cited by this paper
• Endogenous retroviruses function as species-specific enhancer elements in the placenta

  2013influential reference
• Retroviruses facilitate the rapid evolution of the mammalian placenta

  2013cited by this paper
• DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

  2013influential reference
• Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets

  2013cited by this paper
• Fast Computation and Applications of Genome Mappability

  2012cited by this paper
• 29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome

  2012cited by this paper
• Dfam: a database of repetitive DNA based on profile hidden Markov models

  2012cited by this paper
• ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

  2012cited by this paper
• An Integrated Encyclopedia of DNA Elements in the Human Genome

  2012cited by this paper
• Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements.

  2012cited by this paper
• Transposable elements: an abundant and natural source of regulatory sequences for host genes.

  2012cited by this paper
• Prediction of Transposable Element Derived Enhancers Using Chromatin Modification Profiles

  2011cited by this paper
• A high-resolution map of human evolutionary constraint using 29 mammals

  2011cited by this paper
• Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

  2011cited by this paper
• The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

  2011cited by this paper
• FIMO: scanning for occurrences of a given motif

  2011cited by this paper
• The NIH Roadmap Epigenomics Mapping Consortium

  2010cited by this paper
• One Hundred Years of Pleiotropy: A Retrospective

  2010cited by this paper
• Epigenetic histone modifications of human transposable elements: genome defense versus exaptation

  2010cited by this paper
• Origin and evolution of the adaptive immune system: genetic events and selective pressures

  2010cited by this paper
• The regulated retrotransposon transcriptome of mammalian cells

  2009cited by this paper
• Species-Specific Transcription in Mice Carrying Human Chromosome 21

  2008cited by this paper
• Pleiotropic scaling of gene effects and the ‘cost of complexity’

  2008cited by this paper
• HOX Gene Expression

  2007cited by this paper
• Statistical significance for genomewide studies

  2003cited by this paper
• BIOINFORMATICS APPLICATIONS NOTE

  2001cited by this paper
• Developmental basis of limblessness and axial patterning in snakes

  1999cited by this paper
• Interspersed repeats and other mementos of transposable elements in mammalian genomes.

  1999cited by this paper
• Crustacean appendage evolution associated with changes in Hox gene expression

  1997cited by this paper

• The molecular evolution of vertebrate organs.

  2026cites this paper
• Transposable elements as key regulators of placental development

  2025cites this paper
• Gene regulatory innovations from transposable elements in mammalian cerebellum development

  2025influential citation
• Replication rate-information storage trade-off shapes genome architecture across domains

  2025cites this paper
• Analyses of Transposable Elements in Arbuscular Mycorrhizal Fungi Support Evolutionary Parallels With Filamentous Plant Pathogens

  2025cites this paper
• Comparative Analysis of Transposable Element Evolution in Crustaceans

  2025cites this paper
• The emerging sequence grammar of 3D genome organisation

  2025cites this paper
• From Junk DNA to Genomic Treasure: Impacts of Transposable Element DNA, RNA, and Protein in Mammalian Development and Disease

  2025cites this paper
• Genomic profiling of six human somatic histone H1 variants denotes that H1X accumulates at recently incorporated transposable elements

  2024cites this paper
• Accurate allocation of multimapped reads enables regulatory element analysis at repeats

  2024cites this paper
• Natural Transposable Element Insertions Contribute to Host Fitness in Model Yeasts

  2024cites this paper
• Nuclear receptor-SINE B1 network modulates expanded pluripotency in blastoids and blastocysts

  2024cites this paper
• Intrinsically linked lineage-specificity of transposable elements and lncRNAs reshapes transcriptional regulation species- and tissue-specifically

  2024cites this paper
• The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication

  2024cites this paper
• Transposable elements activation triggers necroptosis in mouse embryonic stem cells

  2023cites this paper
• Human Endogenous Retroviruses in Diseases.

  2023cites this paper
• Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats

  2023cites this paper
• Regulatory transposable elements in the encyclopedia of DNA elements

  2023cites this paper
• Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits

  2023influential citation
• Transposable elements as essential elements in the control of gene expression

  2023cites this paper
• Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans

  2023cites this paper
• Roles of transposable elements in the regulation of mammalian transcription

  2022cites this paper
• Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs

  2022cites this paper
• Transposable elements as tissue-specific enhancers in cancers of endodermal lineage

  2022cites this paper
• Mammalian genome innovation through transposon domestication

  2022cites this paper
• Active endogenous retroviral elements in human pluripotent stem cells play a role in regulating host gene expression

  2022cites this paper
• LINE-1 and SINE-B1 mapping and genome diversification in Proechimys species (Rodentia: Echimyidae)

  2022cites this paper
• Clustering of Sex-Biased Genes and Transposable Elements in the Genome of the Medaka Fish Oryzias latipes

  2021cites this paper
• Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

  2021cites this paper
• The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

  2021cites this paper
• Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

  2021cites this paper
• Leftovers of viruses in human physiology

  2021cites this paper
• Modeling the Evolutionary Architectures of Transcribed Human Enhancer Sequences Reveals Distinct Origins, Functions, and Associations with Human Trait Variation

  2021cites this paper
• The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality

  2021cites this paper
• Weak Effect of Gypsy Retrotransposon Bursts on Sonneratia alba Salt Stress Gene Expression

  2021cites this paper
• A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni

  2021cites this paper
• LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

  2021cites this paper
• Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

  2021cites this paper
• Transposable element-derived sequences in vertebrate development

  2021cites this paper
• Role of Transposable Elements in Gene Regulation in the Human Genome

  2020cites this paper
• Epigenetics in age-related macular degeneration: new discoveries and future perspectives

  2020cites this paper
• Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome

  2020cites this paper
• Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes

  2020cites this paper
• Full-length LINE-1s with functional ORFs are favoured by host-level selection in human genomes

  2020cites this paper
• DNA Methylation Repels Binding of HIF Transcription Factors to Maintain Tumour Immunotolerance

  2020cites this paper
• Transposable elements teach T cells new tricks

  2020cites this paper
• LINE elements are a reservoir of regulatory potential in mammalian genomes

  2020cites this paper
• DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance

  2020cites this paper
• Modeling the evolutionary architectures of human enhancer sequences reveals distinct origins, functions, and associations with human-trait variation

  2020influential citation
• Long non-coding RNAs and transposable elements: A functional relationship.

  2020cites this paper
• Regulatory diversity contributes to a divergent transcriptional response to dietary changes in mammals

  2020cites this paper
• Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes.

  2020cites this paper
• Origins and evolutionary consequences of ancient endogenous retroviruses

  2019cites this paper
• The epigenomic landscape of transposable elements across normal human development and anatomy

  2019cites this paper
• Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues

  2019cites this paper
• Transposable elements significantly contributed to the core promoters in the human genome

  2019cites this paper
• Sex and the TEs: transposable elements in sexual development and function in animals

  2019cites this paper
• Independent transposon exaptation is a widespread mechanism of shadow enhancer evolution in the mammalian genome

  2019influential citation
• Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

  2019cites this paper
• Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

  2019cites this paper
• Structure Encoding in DNA.

  2019cites this paper
• Structure Encoding in DNA 1

  2019cites this paper
• Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines

  2019cites this paper
• Actors with Multiple Roles: Pleiotropic Enhancers and the Paradigm of Enhancer Modularity.

  2019cites this paper
• Transposable Elements in the Evolution of Gene Regulatory Networks

  2019cites this paper
• Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs

  2018cites this paper
• Deep learning reveals evolutionary conservation and divergence of sequence properties underlying gene regulatory enhancers across mammals

  2018cites this paper
• Genome-wide maps of distal gene regulatory regions active in the human placenta

  2018cites this paper
• Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

  2018cites this paper
• The impact of endogenous retroviruses on nuclear organization and gene expression

  2018cites this paper
• Transposable elements generate regulatory novelty in a tissue-specific fashion

  2018cites this paper
• Exaptation of transposable element coding sequences.

  2018cites this paper
• Exaptation at the molecular genetic level

  2018cites this paper
• Genome-wide maps of distal gene regulatory enhancers active in the human placenta

  2018cites this paper
• Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

  2018cites this paper
• The placenta goes viral: Retroviruses control gene expression in pregnancy

  2018cites this paper
• Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

  2018cites this paper
• Sequence properties underlying gene regulatory enhancers are conserved across mammals

  2017cites this paper
• Endogenous retroviruses co-opted into divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

  year unknowncites this paper