Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs

Conserved chromosomal functions of RNA interference

(2020) Michael J. Gutbrod et al.   NATURE REVIEWS GENETICS

Transposon age and non-CG methylation

(2020) Zhengming Wang et al.   Nature Communications

Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors

(2020) Brenden Barco et al.   Frontiers in Plant Science

Author Correction: Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

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

(2019) Christopher D Todd et al.   eLife

Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species

(2019) Kaining Hu et al.   BMC BIOINFORMATICS

Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster

(2019) José Luis Villanueva-Cañas et al.   NUCLEIC ACIDS RESEARCH

Expansion of a core regulon by transposable elements promotes Arabidopsis chemical diversity and pathogen defense

(2019) Brenden Barco et al.   Nature Communications

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Environmental and epigenetic regulation of Rider retrotransposons in tomato

(2019) Matthias Benoit et al.   PLoS Genetics

Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

(2019) Pierre Baduel et al.   Nature Communications

Diversification of the Caenorhabditis heat shock response by Helitron transposable elements

(2019) Jacob M Garrigues et al.   eLife

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

(2019) Rita A Batista et al.   eLife

Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

(2019) Pavel Jedlicka et al.   Mobile DNA

Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)

(2018) Jordi Morata et al.   Genome Biology and Evolution

Helraiser intermediates provide insight into the mechanism of eukaryotic replicative transposition

(2018) Ivana Grabundzija et al.   Nature Communications

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

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

(2018) Daniel R Fuentes et al.   eLife

The placenta goes viral: Retroviruses control gene expression in pregnancy

(2018) Edward B. Chuong   PLOS BIOLOGY

Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators

(2018) Daniel Bouyer et al.   PLoS Genetics

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing

(2017) Chun-Wei Yu et al.   PLANT CELL

Systematic dissection of genomic features determining transcription factor binding and enhancer function

(2017) Sharon R. Grossman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

(2017) Diwash Jangam et al.   TRENDS IN GENETICS

Co-option of endogenous viral sequences for host cell function

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

Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

(2017) Irina R. Arkhipova   Mobile DNA

Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis

(2016) Chensi Cao et al.   BMC GENOMICS

How retrotransposons shape genome regulation

(2016) Paolo Mita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Rolling-circle amplification of centromericHelitronsin plant genomes

(2016) Wenwei Xiong et al.   PLANT JOURNAL

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

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes

(2016) Ivana Grabundzija et al.   Nature Communications

DNA Methylation Signatures of the Plant Chromomethyltransferases

(2016) Quentin Gouil et al.   PLoS Genetics

Controlled activation of retrotransposition for plant breeding

(2015) Jerzy Paszkowski   CURRENT OPINION IN BIOTECHNOLOGY

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

(2015) Jose M. Muiño et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Epigenetic regulation and functional exaptation of transposable elements in higher plants

(2014) Xiekui Cui et al.   CURRENT OPINION IN PLANT BIOLOGY

Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage

(2014) Jainy Thomas et al.   Genome Biology and Evolution

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

(2014) Thomas E. Hughes et al.   GENOME RESEARCH

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

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

ATF1 Modulates the Heat Shock Response by Regulating the Stress-Inducible Heat Shock Factor 1 Transcription Complex

(2014) Ryosuke Takii et al.   MOLECULAR AND CELLULAR BIOLOGY

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution ofBrassicaspecies

(2014) Elizabeth Hénaff et al.   PLANT JOURNAL

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

(2014) Florian Maumus et al.   Nature Communications

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity

(2013) Keith R. Oliver et al.   Genome Biology and Evolution

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

Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice

(2013) Kanako Yasuda et al.   MOLECULAR BREEDING

Endogenous retroviruses function as species-specific enhancer elements in the placenta

(2013) Edward B Chuong et al.   NATURE GENETICS

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley 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: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

Photorespiration and the Evolution of C4Photosynthesis

(2012) Rowan F. Sage et al.   Annual Review of Plant Biology

Mechanisms by which transcription factors gain access to target sequence elements in chromatin

(2012) Michael J Guertin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Evolution of Double Positive Autoregulatory Feedback Loops in CYCLOIDEA2 Clade Genes Is Associated with the Origin of Floral Zygomorphy

(2012) X. Yang et al.   PLANT CELL

Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

(2011) Shao-Lun Liu et al.   Genome Biology and Evolution

The C4 plant lineages of planet Earth

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

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

(2011) Vincent J Lynch et al.   NATURE GENETICS

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

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism

(2011) Rajesh Pandey et al.   GENOME BIOLOGY

Studying the Evolution of Promoter Sequences: A Waiting Time Problem

(2010) Sarah Behrens et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ttd1a promoter is involved in DNA–protein binding by salt and light stresses

(2010) Pasqualina Woodrow et al.   MOLECULAR BIOLOGY REPORTS

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

(2010) Galih Kunarso et al.   NATURE GENETICS

Phylogenetic analyses reveal the shady history of C4 grasses

(2010) E. J. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Floral symmetry genes and the origin and maintenance of zygomorphy in a plant-pollinator mutualism

(2010) W. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates

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

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

Atypical E2Fs: new players in the E2F transcription factor family

(2009) Tim Lammens et al.   TRENDS IN CELL BIOLOGY

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

Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA

(2008) Nalini Polavarapu et al.   BMC GENOMICS

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Conserved functions of the pRB and E2F families

(2008) Sander van den Heuvel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY