Regulatory activities of transposable elements: from conflicts to benefits

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

(2016) Katherine B. Chiappinelli et al.   CELL

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer

(2016) Emma C. Scott 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

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Natural courtship song variation caused by an intronic retroelement in an ion channel gene

(2016) Yun Ding et al.   NATURE

Schizophrenia risk from complex variation of complement component 4

(2016) Aswin Sekar et al.   NATURE

Origin and evolution of developmental enhancers in the mammalian neocortex

(2016) Deena Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface

(2016) Leonardo M. R. Ferreira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span inDrosophila

(2016) Jason G. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrotransposons as regulators of gene expression

(2016) R. A. Elbarbary et al.   SCIENCE

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Lessons from Domestication: Targeting Cis -Regulatory Elements for Crop Improvement

(2016) Gwen Swinnen et al.   TRENDS IN PLANT SCIENCE

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

(2016) Rebeca Campos-Sánchez et al.   PLoS Computational Biology

Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate

(2016) Hidenori Nishihara et al.   PLoS Genetics

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Roles for retrotransposon insertions in human disease

(2016) Dustin C. Hancks et al.   Mobile DNA

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues

(2016) Marco De Cecco et al.   Aging-US

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

Pluripotency and the endogenous retrovirus HERVH: Conflict or serendipity?

(2015) Zsuzsanna Izsvák et al.   BIOESSAYS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Critical Role for the DNA Sensor AIM2 in Stem Cell Proliferation and Cancer

(2015) Si Ming Man et al.   CELL

Making Sense of Transcription Networks

(2015) Trevor R. Sorrells et al.   CELL

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

AIM2 inflammasome in infection, cancer, and autoimmunity: Role in DNA sensing, inflammation, and innate immunity

(2015) Si Ming Man et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus

(2015) Shi-Bin Hu et al.   GENES & DEVELOPMENT

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

(2015) Kosuke Hashimoto et al.   GENOME RESEARCH

The potential role of retroviruses in autoimmunity

(2015) Philipp Yu   IMMUNOLOGICAL REVIEWS

Inflammatory response of endothelial cells to a human endogenous retrovirus associated with multiple sclerosis is mediated by TLR4

(2015) Alain Duperray et al.   INTERNATIONAL IMMUNOLOGY

Activation of the innate immune response by endogenous retroviruses

(2015) Tara P. Hurst et al.   JOURNAL OF GENERAL VIROLOGY

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

(2015) Jens Durruthy-Durruthy et al.   NATURE GENETICS

Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

(2015) Nemanja Rodić et al.   NATURE MEDICINE

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The 3D folding of metazoan genomes correlates with the association of similar repetitive elements

(2015) Axel Cournac et al.   NUCLEIC ACIDS RESEARCH

Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma

(2015) A Babaian et al.   ONCOGENE

MIR retrotransposon sequences provide insulators to the human genome

(2015) Jianrong Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retroviral envelope gene captures andsyncytinexaptation for placentation in marsupials

(2015) Guillaume Cornelis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma

(2015) Tara T. Doucet-O'Hare et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Human endogenous retrovirus-K contributes to motor neuron disease

(2015) Wenxue Li et al.   Science Translational Medicine

A family of transposable elements co-opted into developmental enhancers in the mouse neocortex

(2015) James H. Notwell et al.   Nature Communications

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

(2015) Vincent J. Lynch et al.   Cell Reports

Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma

(2015) Ewan A Gibb et al.   Genome Medicine

Partially Redundant Enhancers Cooperatively Maintain Mammalian Pomc Expression Above a Critical Functional Threshold

(2015) Daniel D. Lam et al.   PLoS Genetics

Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

(2015) Christopher E Ellison et al.   eLife

Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family

(2015) Gernot Wolf et al.   Mobile DNA

Long Interspersed Element-1 Protein Expression Is a Hallmark of Many Human Cancers

(2014) Nemanja Rodić et al.   AMERICAN JOURNAL OF PATHOLOGY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Complementary Sequence-Mediated Exon Circularization

(2014) Xiao-Ou Zhang et al.   CELL

Short intronic repeat sequences facilitate circular RNA production

(2014) Dongming Liang et al.   GENES & DEVELOPMENT

Noncoding origins of anthropoid traits and a new null model of transposon functionalization

(2014) Ricardo C.H. del Rosario et al.   GENOME RESEARCH

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Endogenous Retroviruses and the Development of Cancer

(2014) G. Kassiotis   JOURNAL OF IMMUNOLOGY

An Adaptive Transposable Element Insertion in the Regulatory Region of the EO Gene in the Domesticated Silkworm, Bombyx mori

(2014) Wei Sun et al.   MOLECULAR BIOLOGY AND EVOLUTION

The transposable elementBari-Jhehmediates oxidative stress response in Drosophila

(2014) Lain Guio et al.   MOLECULAR ECOLOGY

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang 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 enemy within: endogenous retroelements and autoimmune disease

(2014) Hannah E Volkman et al.   NATURE IMMUNOLOGY

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma

(2014) F. E. Lock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential

(2014) M. Ohnuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

(2014) R. Johnson et al.   RNA

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

(2014) Aurélie Kapusta et al.   TRENDS IN GENETICS

SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age

(2014) Michael Van Meter et al.   Nature Communications

Endogenous Retrovirus Insertion in the KIT Oncogene Determines White and White spotting in Domestic Cats

(2014) Victor A. David et al.   G3-Genes Genomes Genetics

A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila

(2014) Lidia Mateo et al.   PLoS Genetics

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Transposable elements in cancer as a by-product of stress-induced evolvability

(2014) Tobias Mourier et al.   Frontiers in Genetics

Human endogenous retrovirus type W envelope protein inhibits oligodendroglial precursor cell differentiation

(2013) David Kremer et al.   ANNALS OF NEUROLOGY

Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

(2013) Ruchi Shukla et al.   CELL

A Retrotransposon-Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes

(2013) Matyas Flemr et al.   CELL

The role of chromatin insulators in nuclear architecture and genome function

(2013) Kevin Van Bortle et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

Functional microRNAs and target sites are created by lineage-specific transposition

(2013) Ryan M. Spengler et al.   HUMAN MOLECULAR GENETICS

The Role of Transposable Elements in Health and Diseases of the Central Nervous System

(2013) M. T. Reilly et al.   JOURNAL OF NEUROSCIENCE

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

(2013) F. S. J. de Souza et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

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

Activation of transposable elements during aging and neuronal decline in Drosophila

(2013) Wanhe Li et al.   NATURE NEUROSCIENCE

Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets

(2013) Li Teng et al.   NUCLEIC ACIDS RESEARCH

'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

(2013) G. Magiorkinis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transposition-Driven Genomic Heterogeneity in the Drosophila Brain

(2013) P. N. Perrat et al.   SCIENCE

Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network

(2013) C. E. Ellison et al.   SCIENCE

Binding of TFIIIC to SINE Elements Controls the Relocation of Activity-Dependent Neuronal Genes to Transcription Factories

(2013) Luca Crepaldi et al.   PLoS Genetics

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

Long Interspersed Element–1 (LINE-1): Passenger or Driver in Human Neoplasms?

(2013) Nemanja Rodić et al.   PLoS Genetics

The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors

(2012) Alessandro Testori et al.   BMC GENOMICS

Extrathymic Generation of Regulatory T Cells in Placental Mammals Mitigates Maternal-Fetal Conflict

(2012) Robert M. Samstein et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Regulation of transposable elements in maize

(2012) Damon Lisch   CURRENT OPINION IN PLANT BIOLOGY

BRAFV600Eremodels the melanocyte transcriptome and inducesBANCRto regulate melanoma cell migration

(2012) Ross J. Flockhart et al.   GENOME RESEARCH

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Transposon integration enhances expression of stress response genes

(2012) Gang Feng et al.   NUCLEIC ACIDS RESEARCH

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Gene Properties and Chromatin State Influence the Accumulation of Transposable Elements in Genes

(2012) Ying Zhang et al.   PLoS One

29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome

(2012) Craig B. Lowe et al.   PLoS One

Transformation of a transposon into a derived prolactin promoter with function during human pregnancy

(2012) D. Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

C-GATE - catalogue of genes affected by transposable elements

(2012) Rita Rebollo et al.   Mobile DNA

Mobile DNA transposition in somatic cells

(2011) Haig H Kazazian   BMC BIOLOGY

Convergent Evolution of Endometrial Prolactin Expression in Primates, Mice, and Elephants Through the Independent Recruitment of Transposable Elements

(2011) Deena Emera et al.   MOLECULAR BIOLOGY AND EVOLUTION

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Widespread establishment and regulatory impact of Alu exons in human genes

(2011) S. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human endogenous retrovirus type W (HERV-W) in schizophrenia: A new avenue of research at the gene–environment interface

(2011) Marion Leboyer et al.   WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY

Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns

(2011) Ying Zhang et al.   PLoS Computational Biology

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

(2011) Rita Rebollo et al.   PLoS Genetics

The IGF1 small dog haplotype is derived from Middle Eastern grey wolves: a closer look at statistics, sampling, and the alleged Middle Eastern origin of small dogs

(2010) Cornelya FC Klütsch et al.   BMC BIOLOGY

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

(2010) Jennifer C. Chow et al.   CELL

Genomic signatures of germline gene expression

(2010) G. McVicker et al.   GENOME RESEARCH

The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

(2010) E. M. Kvikstad et al.   GENOME RESEARCH

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma

(2010) Björn Lamprecht et al.   NATURE MEDICINE

All y’all need to know ‘bout retroelements in cancer

(2010) Victoria P. Belancio et al.   SEMINARS IN CANCER BIOLOGY

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

(2009) Carla J. Cohen et al.   GENE

Integration target site selection by a resurrected human endogenous retrovirus

(2009) T. Brady et al.   GENES & DEVELOPMENT

Deep homology and the origins of evolutionary novelty

(2009) Neil Shubin et al.   NATURE

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

(2009) Sanzhen Liu et al.   PLoS Genetics

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Retrotransposon Tf1 Is Targeted to Pol II Promoters by Transcription Activators

(2008) Young-Eun Leem et al.   MOLECULAR CELL

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo

(2008) A. C. Roman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Possible involvement of SINEs in mammalian-specific brain formation

(2008) T. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster

(2008) Josefa González et al.   PLOS BIOLOGY