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

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can ENCODE tell us how much junk DNA we carry in our genome?

(2012) Deng-Ke Niu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression

(2012) Ana Ariza-Cosano et al.   BMC GENOMICS

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

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

(2012) Akiko Nakanishi 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

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

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

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

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

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh 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

Prediction of Transposable Element Derived Enhancers Using Chromatin Modification Profiles

(2011) Ahsan Huda et al.   PLoS One

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

Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates

(2011) Keith R Oliver et al.   Mobile DNA

Massive turnover of functional sequence in human and other mammalian genomes

(2010) S. Meader et al.   GENOME RESEARCH

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

Foxa1 Functions as a Pioneer Transcription Factor at Transposable Elements to ActivateAfpduring Differentiation of Embryonic Stem Cells

(2010) Joseph H. Taube et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rodent Evolution: Back to the Root

(2010) Gennady Churakov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

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

Long-range function of an intergenic retrotransposon

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

Transposable element insertions have strongly affected human evolution

(2010) R. J. Britten   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Amaury Herpin et al.   PLoS Genetics

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

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

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

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

(2009) Guillaume Bourque   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2009) Carla J. Cohen et al.   GENE

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

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

A Novel Protein Isoform of the Multicopy Human NAIP Gene Derives from Intragenic Alu SINE Promoters

(2009) Mark T. Romanish 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

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

(2008) Sean B. Carroll   CELL

Transposable elements as drivers of genomic and biological diversity in vertebrates

(2008) Astrid Böhne et al.   CHROMOSOME RESEARCH

A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity

(2008) A. M. Smith et al.   GENOME RESEARCH

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Neutralism and selectionism: a network-based reconciliation

(2008) Andreas Wagner   NATURE REVIEWS GENETICS

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