Emerging roles for endogenous retroviruses in immune epigenetic regulation*

A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection

(2021) Cornelia Blume et al.   NATURE GENETICS

B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and Histone Modifications in the Mouse

(2021) Tomoko Ichiyanagi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic properties of variably methylated retrotransposons in mouse

(2021) Jessica L. Elmer et al.   Mobile DNA

Viruses and Endogenous Retroviruses as Roots for Neuroinflammation and Neurodegenerative Diseases

(2021) Christine Römer   Frontiers in Neuroscience

Switching Sides: How Endogenous Retroviruses Protect us from Viral Infections

(2021) Smitha Srinivasachar Badarinarayan et al.   JOURNAL OF VIROLOGY

Epigenetically regulated digital signaling defines epithelial innate immunity at the tissue level

(2021) Helen R. Clark et al.   Nature Communications

The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination

(2021) Florian Wimmers et al.   CELL

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration

(2021) Thomas Clapes et al.   NATURE CELL BIOLOGY

Cas9 targeted enrichment of mobile elements using nanopore sequencing

(2021) Torrin L. McDonald et al.   Nature Communications

High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

(2021) Sarah E. Pierce et al.   Nature Communications

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

Contribution of unfixed transposable element insertions to human regulatory variation

(2020) Clément Goubert et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An atlas of transposable element-derived alternative splicing in cancer

(2020) Evan A. Clayton et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transposable elements have contributed human regulatory regions that are activated upon bacterial infection

(2020) Lucia Bogdan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

(2020) Qihui Wang et al.   CELL

Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China

(2020) Chuan Qin et al.   CLINICAL INFECTIOUS DISEASES

Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers

(2020) Mengliang Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage

(2020) Gernot Wolf et al.   eLife

Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option

(2020) Kevin W. Ng et al.   NATURE GENETICS

Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor

(2020) Olusegun O. Onabajo et al.   NATURE GENETICS

HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression

(2020) Smitha Srinivasachar Badarinarayan et al.   NUCLEIC ACIDS RESEARCH

Regulation of Expression and Latency in BLV and HTLV

(2020) Aneta Pluta et al.   Viruses-Basel

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

(2020) Adam D. Ewing et al.   MOLECULAR CELL

The emerging role of epigenetics in human autoimmune disorders

(2019) Roberta Mazzone et al.   Clinical Epigenetics

Author Correction: Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

Expression of endogenous retroviruses reflects increased usage of atypical enhancers in T cells

(2019) Saliha Azébi et al.   EMBO JOURNAL

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells

(2019) Christopher D Todd et al.   eLife

The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition

(2019) Serge Nataf et al.   Frontiers in Genetics

Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations

(2019) Jerzy K. Kulski   Cells

pHERV-W envelope protein fuels microglial cell-dependent damage of myelinated axons in multiple sclerosis

(2019) David Kremer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endogenous Retrovirus-Derived Long Noncoding RNA Enhances Innate Immune Responses via Derepressing RELA Expression

(2019) Bin Zhou et al.   mBio

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity

(2019) Nora Schmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

ImmGen report: sexual dimorphism in the immune system transcriptome

(2019) Shani Talia Gal-Oz et al.   Nature Communications

The epigenomic landscape of transposable elements across normal human development and anatomy

(2019) Erica C. Pehrsson et al.   Nature Communications

Single-Cell Expression Variability Implies Cell Function

(2019) Daniel Osorio et al.   Cells

The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes

(2018) Luisa Robbez-Masson et al.   GENOME RESEARCH

Estrogen‐dependent control and cell‐to‐cell variability of transcriptional bursting

(2018) Christoph Fritzsch et al.   Molecular Systems Biology

Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses

(2018) Israel Cañadas et al.   NATURE MEDICINE

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise

(2018) Victor C. Wong et al.   Cell Reports

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

(2018) Charles G. Danko et al.   Nature Ecology & Evolution

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Anthropoid primate–specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length

(2018) Caitlin E. Dunn-Fletcher et al.   PLOS BIOLOGY

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance

(2018) Anastasiya Kazachenka et al.   CELL

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

Alu insertion variants alter mRNA splicing

(2018) Lindsay M Payer et al.   NUCLEIC ACIDS RESEARCH

ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses

(2018) Maria Tokuyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

(2018) Stefanie Schöne et al.   PLoS Genetics

Transposable elements are the primary source of novelty in primate gene regulation

(2017) Marco Trizzino et al.   GENOME RESEARCH

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer

(2017) Frances E. Lock et al.   PLoS One

The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution

(2017) Peng Yang et al.   TRENDS IN GENETICS

Transposable Elements Direct The Coevolution between Plants and Microbes

(2017) Michael F. Seidl et al.   TRENDS IN GENETICS

The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity

(2017) Christina Ernst et al.   Nature Communications

Co-option of endogenous viral sequences for host cell function

(2017) John A .Frank et al.   Current Opinion in Virology

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses

(2017) Andrew E. Shaw et al.   PLOS BIOLOGY

Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses

(2017) Jumpei Ito et al.   PLoS Genetics

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

(2016) Katherine B. Chiappinelli et al.   CELL

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

MSRV envelope protein is a potent, endogenous and pathogenic agonist of human toll-like receptor 4: Relevance of GNbAC1 in multiple sclerosis treatment

(2016) Alexandra Madeira et al.   JOURNAL OF NEUROIMMUNOLOGY

NF-κB and IRF1 Induce Endogenous Retrovirus K Expression via Interferon-Stimulated Response Elements in Its 5′ Long Terminal Repeat

(2016) Mamneet Manghera et al.   JOURNAL OF VIROLOGY

Schizophrenia risk from complex variation of complement component 4

(2016) Aswin Sekar 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

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

HIV integration and the establishment of latency in CCL19-treated resting CD4+ T cells require activation of NF-κB

(2016) Suha Saleh et al.   Retrovirology

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

(2016) E. B. Chuong et al.   SCIENCE

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells

(2016) Marius Walter et al.   eLife

Endogenous retroviral promoter exaptation in human cancer

(2016) Artem Babaian et al.   Mobile DNA

Variation is function: Are single cell differences functionally important?

(2015) Hannah Dueck et al.   BIOESSAYS

Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

(2015) Bin Xia Yang et al.   CELL

Noise Facilitates Transcriptional Control under Dynamic Inputs

(2015) Ryan A. Kellogg et al.   CELL

Beyond receptors and signaling: epigenetic factors in the regulation of innate immunity

(2015) Stuti Mehta et al.   IMMUNOLOGY AND CELL BIOLOGY

Fighting Fire with Fire: Endogenous Retrovirus Envelopes as Restriction Factors

(2015) Ray Malfavon-Borja et al.   JOURNAL OF VIROLOGY

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

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

Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells

(2015) I. A. Tchasovnikarova et al.   SCIENCE

ImmVar project: Insights and design considerations for future studies of “healthy” immune variation

(2015) Philip L. De Jager et al.   SEMINARS IN IMMUNOLOGY

Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages

(2015) Xiaoyu Zhuo et al.   PLoS Pathogens

Epigenetic Heterogeneity in HIV-1 Latency Establishment

(2015) Yuka Matsuda et al.   Scientific Reports

Chromatin Contributions to the Regulation of Innate Immunity

(2014) Stephen T. Smale et al.   Annual Review of Immunology

Cytotoxicity of Human Endogenous Retrovirus K-Specific T Cells toward Autologous Ovarian Cancer Cells

(2014) K. Rycaj et al.   CLINICAL CANCER RESEARCH

Low HERV-K(C4) Copy Number Is Associated With Type 1 Diabetes

(2014) Mike J. Mason et al.   DIABETES

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

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

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

Heterogeneity in immune responses: from populations to single cells

(2014) Rahul Satija et al.   TRENDS IN IMMUNOLOGY

Regulation of Human T-Lymphotropic Virus Type I Latency and Reactivation by HBZ and Rex

(2014) Subha Philip et al.   PLoS Pathogens

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

DNA methylation modulates HRES1/p28 expression in B cells from patients with Lupus

(2013) Tinhinane Fali et al.   AUTOIMMUNITY

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts

(2013) José Viñuelas et al.   BMC BIOLOGY

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation

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

An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication

(2013) T. Tsuchiya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endogenous retrovirus-K promoter: a landing strip for inflammatory transcription factors?

(2013) Mamneet Manghera et al.   Retrovirology

HIV-1 transcription and latency: an update

(2013) Carine Van Lint et al.   Retrovirology

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Rules of Engagement: Molecular Insights from Host-Virus Arms Races

(2012) Matthew D. Daugherty et al.   Annual Review of Genetics

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

(2012) Dominic Schmidt et al.   CELL

Dynamic roles for NF-κB in HTLV-I and HIV-1 retroviral pathogenesis

(2012) Jonathan K. Chan et al.   IMMUNOLOGICAL REVIEWS

Expression of HERV-Fc1, a Human Endogenous Retrovirus, Is Increased in Patients with Active Multiple Sclerosis

(2012) M. J. Laska et al.   JOURNAL OF VIROLOGY

Studies of endogenous retroviruses reveal a continuing evolutionary saga

(2012) Jonathan P. Stoye   NATURE REVIEWS MICROBIOLOGY

The endogenous retroviral envelope protein syncytin-1 inhibits LPS/PHA-stimulated cytokine responses in human blood and is sorted into placental exosomes

(2012) J.M. Tolosa et al.   PLACENTA

Env-less endogenous retroviruses are genomic superspreaders

(2012) G. Magiorkinis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endogenous retrovirus sequences as a novel class of tumor-specific antigens: an example of HERV-H env encoding strong CTL epitopes

(2011) Christina S. Mullins et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Coevolution of retroelements and tandem zinc finger genes

(2011) J. H. Thomas et al.   GENOME RESEARCH

The Etiology of Multiple Sclerosis: Genetic Evidence for the Involvement of the Human Endogenous Retrovirus HERV-Fc1

(2011) Bjørn A. Nexø et al.   PLoS One

Transcriptional Bursting from the HIV-1 Promoter Is a Significant Source of Stochastic Noise in HIV-1 Gene Expression

(2010) Abhyudai Singh et al.   BIOPHYSICAL JOURNAL

Retroviral reverse transcriptases

(2010) Alon Herschhorn et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Adaptive Evolution of Mus Apobec3 Includes Retroviral Insertion and Positive Selection at Two Clusters of Residues Flanking the Substrate Groove

(2010) Bradley Sanville et al.   PLoS Pathogens

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

(2009) Carla J. Cohen et al.   GENE

Novel reliable real-time PCR for differential detection of MSRVenv and syncytin-1 in RNA and DNA from patients with multiple sclerosis

(2009) Giuseppe Mameli et al.   JOURNAL OF VIROLOGICAL METHODS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Molecular control of HIV-1 postintegration latency: implications for the development of new therapeutic strategies

(2009) Laurence Colin et al.   Retrovirology

B cells and monocytes from patients with active multiple sclerosis exhibit increased surface expression of both HERV-H Env and HERV-W Env, accompanied by increased seroreactivity

(2009) Tomasz Brudek et al.   Retrovirology

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Stochasticity and Cell Fate

(2008) R. Losick et al.   SCIENCE