Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates

HTT-DB: Horizontally transferred transposable elements database: Fig. 1.

(2015) Bruno Reis Dotto et al.   BIOINFORMATICS

Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon

(2015) Vladimir V Kapitonov et al.   Biology Direct

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

(2015) Gennadi V. Glinsky   Genome Biology and Evolution

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

(2015) Eric Londin 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

Selective expression of sense and antisense transcripts of the sushi-ichi-related retrotransposon – derived family during mouse placentogenesis

(2015) Christine Henke et al.   Retrovirology

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

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

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Repeated horizontal transfers of four DNA transposons in invertebrates and bats

(2015) Zhou Tang et al.   Mobile DNA

The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human

(2015) Sheng Qin et al.   PLoS One

The Captured Retroviral Envelope syncytin-A and syncytin-B Genes Are Conserved in the Spalacidae Together with Hemotrichorial Placentation1

(2014) Cécile Vernochet et al.   BIOLOGY OF REPRODUCTION

Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage

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

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

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

(2014) S. Washietl et al.   GENOME RESEARCH

RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species

(2014) Anne-Marie Dion-Côté et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Jichang Wang et al.   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea 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

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs

(2014) G. Cornelis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

(2014) Alexander Hayward 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

Transcriptional regulatory functions of nuclear long noncoding RNAs

(2014) Keith W. Vance et al.   TRENDS IN GENETICS

The evolution of cichlid fish egg-spots is linked with a cis-regulatory change

(2014) M. Emília Santos et al.   Nature Communications

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution

(2013) Atma M. Ivancevic et al.   BIOESSAYS

Origin and Evolution of Yolk Proteins: Expansion and Functional Diversification of Large Lipid Transfer Protein Superfamily1

(2013) Long Tao Wu et al.   BIOLOGY OF REPRODUCTION

Systematic classification of non-coding RNAs by epigenomic similarity

(2013) Mikhail G Dozmorov et al.   BMC BIOINFORMATICS

ANRIL/CDKN2B-AS shows two-stage clade-specific evolution and becomes conserved after transposon insertions in simians

(2013) Sha He et al.   BMC EVOLUTIONARY BIOLOGY

Inferring the expression variability of human transposable element-derived exons by linear model analysis of deep RNA sequencing data

(2013) Wensheng Zhang et al.   BMC GENOMICS

Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective

(2013) P. P. Amaral et al.   Briefings in Functional Genomics

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Identification and Evolution of the Silkworm Helitrons and their Contribution to Transcripts

(2013) M.-J. Han et al.   DNA RESEARCH

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

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

Genesis and Regulatory Wiring of Retroelement-Derived Domesticated Genes: A Phylogenomic Perspective

(2013) Janez Kokošar et al.   MOLECULAR 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

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

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

(2013) Edward B Chuong et al.   NATURE GENETICS

Captured retroviral envelope syncytin gene associated with the unique placental structure of higher ruminants

(2013) Guillaume Cornelis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

The Vast, Conserved Mammalian lincRNome

(2013) David Managadze et al.   PLoS Computational Biology

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

(2013) Aurélie Kapusta et al.   PLoS Genetics

Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks

(2013) Lesca M. Holdt 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

Transposable element recruitments in the mammalian placenta: impacts and mechanisms

(2012) D. Emera et al.   Briefings in Functional Genomics

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

(2012) Dominic Schmidt et al.   CELL

Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives

(2012) Gabriel Luz Wallau et al.   Genome Biology and Evolution

Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback

(2012) Eryn Blass et al.   Genome Biology and Evolution

Birth and expression evolution of mammalian microRNA genes

(2012) J. Meunier et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Evolution of the Australian Lungfish (Neoceratodus forsteri) Genome: A Major Role for CR1 and L2 LINE Elements

(2012) C. J. Metcalfe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Transposable elements domesticated and neofunctionalized by eukaryotic genomes

(2012) Ahmed M. Alzohairy et al.   PLASMID

A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8

(2012) Akiko Nakanishi et al.   PLoS One

A Fish-Specific Transposable Element Shapes the Repertoire of p53 Target Genes in Zebrafish

(2012) Lucia Micale 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

Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy

(2012) F. Cartault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancestral capture of syncytin-Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora

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

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

The role of genes domesticated from LTR retrotransposons and retroviruses in mammals

(2012) Tomoko Kaneko-Ishino et al.   Frontiers in Microbiology

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

(2012) David Kelley et al.   GENOME BIOLOGY

V(D)J Recombination: Mechanisms of Initiation

(2011) David G. Schatz et al.   Annual Review of Genetics

Exonization of transposed elements: A challenge and opportunity for evolution

(2011) Jürgen Schmitz et al.   BIOCHIMIE

Impact of Alu repeats on the evolution of human p53 binding sites

(2011) Feng Cui et al.   Biology Direct

SASPase regulates stratum corneum hydration through profilaggrin-to-filaggrin processing

(2011) Takeshi Matsui et al.   EMBO Molecular Medicine

A single nucleotide polymorphism in a miR-1302 binding site in CGA increases the risk of idiopathic male infertility

(2011) Hao Zhang et al.   FERTILITY AND STERILITY

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch

(2011) A. C. Roman et al.   GENOME RESEARCH

Retrofitting the Genome: L1 Extinction Follows Endogenous Retroviral Expansion in a Group of Muroid Rodents

(2011) I. K. Erickson et al.   JOURNAL OF VIROLOGY

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

Tracking the Ancestry of a Deeply Conserved Eumetazoan SINE Domain

(2011) O. Piskurek et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human piRNAs Are Under Selection in Africans and Repress Transposable Elements

(2011) S. Lukic et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles

(2011) C. Gilbert et al.   MOLECULAR 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

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

Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

(2011) L. F. Franchini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

Origin and evolution of a placental-specific microRNA family in the human genome

(2010) Zhidong Yuan et al.   BMC EVOLUTIONARY BIOLOGY

Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri

(2010) Corey T Watson et al.   BMC EVOLUTIONARY BIOLOGY

The rapid generation of chimerical genes expanding protein diversity in zebrafish

(2010) Beide Fu et al.   BMC GENOMICS

Genome Size and Species Diversification

(2010) Ken Kraaijeveld   Evolutionary Biology

XLMR candidate mouse gene, Zcchc12 (Sizn1) is a novel marker of Cajal–Retzius cells

(2010) Ginam Cho et al.   GENE EXPRESSION PATTERNS

Pervasive Horizontal Transfer of Rolling-Circle Transposons among Animals

(2010) Jainy Thomas et al.   Genome Biology and Evolution

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Rapid Sequence and Expression Divergence Suggest Selection for Novel Function in Primate-Specific KRAB-ZNF Genes

(2010) K. Nowick et al.   MOLECULAR BIOLOGY AND EVOLUTION

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

(2010) Clément Gilbert et al.   NATURE

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

Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

(2010) Christopher E. Mason et al.   NUCLEIC ACIDS RESEARCH

Characteristics of Transposable Element Exonization within Human and Mouse

(2010) Noa Sela et al.   PLoS One

Uniquely human evolution of sialic acid genetics and biology

(2010) A. Varki   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements

(2010) Amaury Herpin et al.   PLoS Genetics

Cloning, Characterization, and Expression Analysis of the Novel Acetyltransferase Retrogene Ard1b in the Mouse1

(2009) Alan Lap-Yin Pang et al.   BIOLOGY OF REPRODUCTION

Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates

(2009) Adrian F Gombart et al.   BMC GENOMICS

Molecular domestication of transposable elements: From detrimental parasites to useful host genes

(2009) L. Sinzelle et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transposable elements in gene regulation and in the evolution of vertebrate genomes

(2009) Guillaume Bourque   CURRENT OPINION IN GENETICS & DEVELOPMENT

Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes

(2009) Lan Lin et al.   HUMAN MOLECULAR GENETICS

Segmental copy number variation shapes tissue transcriptomes

(2009) Charlotte N Henrichsen et al.   NATURE GENETICS

p53 responsive elements in human retrotransposons

(2009) C R Harris et al.   ONCOGENE

Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

(2009) Deng Pan et al.   PLoS One

The role of transposable elements in the regulation of IFN-λ1 gene expression

(2009) Scott J. P. Thomson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of an endogenous retroviral envelope gene with fusogenic activity and placenta-specific expression in the rabbit: a new "syncytin" in a third order of mammals

(2009) Odile Heidmann et al.   Retrovirology

The emergence of new genes on the young therian X

(2009) Lukasz Potrzebowski et al.   TRENDS IN GENETICS

Adaptive Evolution in Zinc Finger Transcription Factors

(2009) Ryan O. Emerson et al.   PLoS Genetics

Evidence thatSIZN1is a candidate X-linked mental retardation gene

(2008) Ginam Cho et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Transposable elements as drivers of genomic and biological diversity in vertebrates

(2008) Astrid Böhne et al.   CHROMOSOME RESEARCH

The impact of multiple splice sites in human L1 elements

(2008) V.P. Belancio et al.   GENE

Loss of LINE-1 Activity in the Megabats

(2008) Michael A. Cantrell et al.   GENETICS

Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus

(2008) D. A. Ray et al.   GENOME RESEARCH

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Using Alu Elements as Polyadenylation Sites: A Case of Retroposon Exaptation

(2008) C. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta

(2008) Yoichi Sekita et al.   NATURE GENETICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes

(2008) Ju Youn Lee et al.   NUCLEIC ACIDS RESEARCH

A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements

(2008) Eugeny A. Elisaphenko et al.   PLoS One

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

Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish

(2008) Z. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes

(2008) Lukasz Potrzebowski et al.   PLOS BIOLOGY

Functional diversification of duplicate genes through subcellular adaptation of encoded proteins

(2008) Ana C Marques et al.   GENOME BIOLOGY