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

The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

(2013) Phillip Grote et al.   DEVELOPMENTAL CELL

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

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

(2012) Dominic Schmidt et al.   CELL

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

BRAFV600Eremodels the melanocyte transcriptome and inducesBANCRto regulate melanoma cell migration

(2012) Ross J. Flockhart 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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Endogenous viruses: insights into viral evolution and impact on host biology

(2012) Cédric Feschotte et al.   NATURE REVIEWS GENETICS

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

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

(2012) L. D. Ward et al.   SCIENCE

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

(2012) Claudia Kutter et al.   PLoS Genetics

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

(2012) David Kelley et al.   GENOME BIOLOGY

Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk

(2011) Guangfu Jin et al.   CARCINOGENESIS

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

Genome-wide prediction and analysis of human chromatin boundary elements

(2011) Jianrong Wang et al.   NUCLEIC ACIDS RESEARCH

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

Silencing of endogenous retroviruses: when and why do histone marks predominate?

(2011) Danny C. Leung et al.   TRENDS IN BIOCHEMICAL SCIENCES

Dynamic control of endogenous retroviruses during development

(2011) Helen M. Rowe et al.   VIROLOGY

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

DARNED: a DAtabase of RNa EDiting in humans

(2010) A. Kiran et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats

(2010) Ling-Ling Chen et al.   CELL CYCLE

Role of H3K27 methylation in the regulation of lncRNA expression

(2010) Susan C Wu et al.   CELL RESEARCH

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

(2010) D. Xie et al.   GENOME RESEARCH

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

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

Genome-wide computational identification and manual annotation of human long noncoding RNA genes

(2010) H. Jia et al.   RNA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting 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

Genome-Wide Identification of Long Noncoding RNAs in CD8+ T Cells

(2009) K. C. Pang et al.   JOURNAL OF IMMUNOLOGY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

Retroviral promoters in the human genome

(2008) Andrew B. Conley et al.   BIOINFORMATICS

UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion

(2008) Fan Wang et al.   FEBS LETTERS

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

MEN  /  nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

(2008) H. Sunwoo et al.   GENOME RESEARCH

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

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

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA