Transposable elements generate regulatory novelty in a tissue-specific fashion

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs

(2018) Michelle C Ward et al.   eLife

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

(2017) Marco Trizzino et al.   GENOME RESEARCH

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Detection of the LINE-1 retrotransposon RNA-binding protein ORF1p in different anatomical regions of the human brain

(2017) Debpali Sur et al.   Mobile DNA

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis

(2016) Shi Chi Leow et al.   DEVELOPMENT

The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes

(2016) Václav Janoušek et al.   Genome Biology and Evolution

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

(2016) E. B. Chuong et al.   SCIENCE

Massive contribution of transposable elements to mammalian regulatory sequences

(2016) Nirmala Arul Rayan et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Chromatin variation associated with liver metabolism is mediated by transposable elements

(2016) Juan Du et al.   Epigenetics & Chromatin

Ubiquitous L1 Mosaicism in Hippocampal Neurons

(2015) Kyle R. Upton et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

CPEB1 mediates epithelial-to-mesenchyme transition and breast cancer metastasis

(2015) K Nagaoka et al.   ONCOGENE

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

T-bet and Eomes instruct the development of two distinct natural killer cell lineages in the liver and in the bone marrow

(2014) Cécile Daussy et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network

(2014) Carine Gubelmann et al.   eLife

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

Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells

(2013) Nina V Fuchs et al.   Retrovirology

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

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

(2012) Dominic Schmidt et al.   CELL

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

Cytoplasmic Polyadenylation Element Binding Protein Deficiency Stimulates PTEN and Stat3 mRNA Translation and Induces Hepatic Insulin Resistance

(2012) Ilya M. Alexandrov et al.   PLoS Genetics

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

(2011) Vincent J Lynch et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck et al.   CELL

NF-κB and STAT3 – key players in liver inflammation and cancer

(2010) Guobin He et al.   CELL RESEARCH

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

(2010) Galih Kunarso et al.   NATURE GENETICS

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

(2009) Carla J. Cohen et al.   GENE

Estrogen-induced interaction between KLF5 and estrogen receptor (ER) suppresses the function of ER in ER-positive breast cancer cells

(2009) Peng Guo et al.   INTERNATIONAL JOURNAL OF CANCER

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The ZEB1 Transcription Factor Is a Novel Repressor of Adiposity in Female Mice

(2009) Jessica N. Saykally et al.   PLoS One

ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth

(2009) Ellen Markljung et al.   PLOS BIOLOGY

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

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