Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

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

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

Regulatory activities of transposable elements: from conflicts to benefits

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

Origin and evolution of developmental enhancers in the mammalian neocortex

(2016) Deena Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) E. B. Chuong et al.   SCIENCE

Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer

(2016) Nicholas C. Gomez et al.   Cell Reports

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Detecting Endogenous Retrovirus-Driven Tissue-Specific Gene Transcription

(2015) Mihaela Pavlicev 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

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

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

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

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape

(2013) Mingchao Xie et al.   NATURE GENETICS

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

(2013) Edward B Chuong et al.   NATURE GENETICS

Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets

(2013) Li Teng et al.   NUCLEIC ACIDS RESEARCH

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

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien 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

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

(2012) John A. Capra et al.   PLoS Computational Biology

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Prediction of Transposable Element Derived Enhancers Using Chromatin Modification Profiles

(2011) Ahsan Huda et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

One Hundred Years of Pleiotropy: A Retrospective

(2010) F. W. Stearns   GENETICS

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Epigenetic histone modifications of human transposable elements: genome defense versus exaptation

(2010) Ahsan Huda et al.   Mobile DNA

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Origin and evolution of the adaptive immune system: genetic events and selective pressures

(2009) Martin F. Flajnik et al.   NATURE REVIEWS GENETICS

Pleiotropic scaling of gene effects and the ‘cost of complexity’

(2008) Günter P. Wagner et al.   NATURE

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE