Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly

What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation

(2020) Michelle Percharde et al.   BIOESSAYS

Ectopic expression of the Stabilin2 gene triggered by an intracisternal A particle (IAP) element in DBA/2J strain of mice

(2020) Nobuyo Maeda-Smithies et al.   MAMMALIAN GENOME

Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication

(2020) Daniel Ardeljan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

On transposons and totipotency

(2020) Maria-Elena Torres-Padilla   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Susceptibility Locus on Chromosome 13 Profoundly Impacts the Stability of Genomic Imprinting in Mouse Pluripotent Stem Cells

(2020) Emily Swanzey et al.   Cell Reports

Is imprinting the result of “friendly fire” by the host defense system?

(2020) Miroslava Ondičová et al.   PLoS Genetics

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

(2020) Gernot Wolf et al.   eLife

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage

(2020) Rajini Srinivasan et al.   Science Advances

Transposable Elements: A Common Feature of Neurodevelopmental and Neurodegenerative Disorders

(2020) Marie E. Jönsson et al.   TRENDS IN GENETICS

Inter-Strain Epigenomic Profiling Reveals a Candidate IAP Master Copy in C3H Mice

(2020) Rita Rebollo et al.   Viruses-Basel

Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers

(2020) Jessica L. Elmer et al.   Viruses-Basel

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia

(2020) Özgen Deniz et al.   Nature Communications

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

(2020) Celia Alda-Catalinas et al.   Cell Systems

ZNF445 is a primary regulator of genomic imprinting

(2019) Nozomi Takahashi et al.   GENES & DEVELOPMENT

An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos

(2019) Longqi Liu et al.   Nature Communications

Author Correction: Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

The Lupus Susceptibility Locus Sgp3 Encodes the Suppressor of Endogenous Retrovirus Expression SNERV

(2019) Rebecca S. Treger et al.   IMMUNITY

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program

(2019) Mélanie Eckersley-Maslin et al.   GENES & DEVELOPMENT

The KRAB-Zinc finger protein ZFP708 mediates epigenetic repression at RMER19B retrotransposons

(2019) Michelle K. Y. Seah et al.   DEVELOPMENT

DPPA2 and DPPA4 are necessary to establish a 2C‐like state in mouse embryonic stem cells

(2019) Alberto De Iaco et al.   EMBO REPORTS

LINE-1 Evasion of Epigenetic Repression in Humans

(2019) Francisco J. Sanchez-Luque et al.   MOLECULAR CELL

Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes

(2019) Weiyu Zhang et al.   NUCLEIC ACIDS RESEARCH

Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors

(2019) Marie E Jönsson et al.   Nature Communications

Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease

(2019) Oliver H. Tam et al.   Mobile DNA

The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals

(2019) Melania Bruno et al.   Annual Review of Genetics

Xist RNA in action: Past, present, and future

(2019) Agnese Loda et al.   PLoS Genetics

Environmental and epigenetic regulation of Rider retrotransposons in tomato

(2019) Matthias Benoit et al.   PLoS Genetics

The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome

(2019) Olympia Gianfrancesco et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Soluble PD-L1 generated by endogenous retroelement exaptation is a receptor antagonist

(2019) Kevin W Ng et al.   eLife

Evolution of imprinting via lineage-specific insertion of retroviral promoters

(2019) Aaron B. Bogutz et al.   Nature Communications

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

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

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells

(2018) Kei Fukuda et al.   GENOME RESEARCH

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

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

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

(2018) Melanie A. Eckersley-Maslin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Neuropathic MORC2 mutations perturb GHKL ATPase dimerization dynamics and epigenetic silencing by multiple structural mechanisms

(2018) Christopher H. Douse et al.   Nature Communications

A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing

(2018) Masaki Kato et al.   Nature Communications

Human Endogenous Retroviruses and Their Putative Role in the Development of Autoimmune Disorders Such as Multiple Sclerosis

(2018) Victoria Gröger et al.   Frontiers in Microbiology

KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control

(2018) Christopher HC Tie et al.   EMBO REPORTS

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

(2018) Jingtao Lilue et al.   NATURE GENETICS

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

(2018) Anastasiya Kazachenka et al.   CELL

LTRs activated by Epstein-Barr virus–induced transformation of B cells alter the transcriptome

(2018) Amy Leung et al.   GENOME RESEARCH

NP220 mediates silencing of unintegrated retroviral DNA

(2018) Yiping Zhu et al.   NATURE

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

(2017) Marco Trizzino et al.   GENOME RESEARCH

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

(2017) Nian Liu et al.   NATURE

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Hyperactivation of HUSH complex function by Charcot–Marie–Tooth disease mutation in MORC2

(2017) Iva A Tchasovnikarova et al.   NATURE GENETICS

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

DUX-family transcription factors regulate zygotic genome activation in placental mammals

(2017) Alberto De Iaco et al.   NATURE GENETICS

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

(2017) Peter G Hendrickson et al.   NATURE GENETICS

The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses

(2017) Barbara Hummel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses

(2017) Barbara Hummel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

How to tame an endogenous retrovirus: HERVH and the evolution of human pluripotency

(2017) Christine Römer et al.   Current Opinion in Virology

Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues

(2016) Gabriela Ecco et al.   DEVELOPMENTAL CELL

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

(2016) Peter J. Thompson et al.   MOLECULAR CELL

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

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

(2016) E. B. Chuong et al.   SCIENCE

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs

(2016) Mélanie A. Eckersley-Maslin et al.   Cell Reports

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

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

Endogenous retroviral promoter exaptation in human cancer

(2016) Artem Babaian et al.   Mobile DNA

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

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

(2015) Ahmet M. Denli et al.   CELL

The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses

(2015) Gernot Wolf et al.   GENES & DEVELOPMENT

DNA methylation modulates HERV-E expression in CD4+ T cells from systemic lupus erythematosus patients

(2015) Zhouwei Wu et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes

(2015) Patrick L. Collins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrotransposons shape species-specific embryonic stem cell gene expression

(2015) Luisa Robbez-Masson et al.   Retrovirology

The decline of human endogenous retroviruses: extinction and survival

(2015) Gkikas Magiorkinis et al.   Retrovirology

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

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

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

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

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

(2015) Liana Fasching et al.   Cell Reports

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

(2015) Ruslan Strogantsev et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

Types of DNA methylation status of the interspersed repetitive sequences for LINE-1, Alu, HERV-E and HERV-K in the neutrophils from systemic lupus erythematosus patients and healthy controls

(2014) Patadon Sukapan et al.   JOURNAL OF HUMAN GENETICS

The first mouse mutants of D14Abb1e (Fam208a) show that it is critical for early development

(2014) Sarah K. Harten et al.   MAMMALIAN GENOME

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

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

Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma

(2014) Stephan Kreher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET

(2013) H. M. Rowe et al.   DEVELOPMENT

The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option

(2013) Aaron M. Wenger et al.   PLoS Genetics

DUX4 Binding to Retroelements Creates Promoters That Are Active in FSHD Muscle and Testis

(2013) Janet M. Young et al.   PLoS Genetics

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

(2012) Robert M. Samstein et al.   CELL

TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells

(2012) H. M. Rowe et al.   GENOME RESEARCH

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

(2012) K. Schroder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Christoffer Nellåker 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

Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression

(2011) Daudi Jjingo et al.   Genome Biology and Evolution

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Genomic imprinting: the emergence of an epigenetic paradigm

(2011) Anne C. Ferguson-Smith   NATURE REVIEWS GENETICS

A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons

(2011) Kensuke Tashiro et al.   PLoS One

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

(2011) Rita Rebollo et al.   PLoS Genetics

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Jennifer C. Chow et al.   CELL

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

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

(2010) Björn Lamprecht et al.   NATURE MEDICINE

Functional Comparison of Innate Immune Signaling Pathways in Primates

(2010) Luis B. Barreiro et al.   PLoS Genetics

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

An infectious progenitor for the murine IAP retrotransposon: Emergence of an intracellular genetic parasite from an ancient retrovirus

(2008) D. Ribet et al.   GENOME RESEARCH

Satb2 Regulates Callosal Projection Neuron Identity in the Developing Cerebral Cortex

(2008) Elizabeth A. Alcamo et al.   NEURON

TRIM28 mediates primer binding site-targeted silencing of Lys1,2 tRNA-utilizing retroviruses in embryonic cells

(2008) D. Wolf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA