Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs

(2016) Gali Housman et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

(2016) Sungyul Lee et al.   CELL

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

(2016) Jeffrey J. Quinn et al.   GENES & DEVELOPMENT

Unlinking an lncRNA from Its Associated cis Element

(2016) Vikram R. Paralkar et al.   MOLECULAR CELL

Endogenous microRNA sponges: evidence and controversy

(2016) Daniel W. Thomson et al.   NATURE REVIEWS GENETICS

Function and evolution of local repeats in the Firre locus

(2016) Ezgi Hacisuleyman et al.   Nature Communications

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

(2016) Ailone Tichon et al.   Nature Communications

Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex

(2015) Adam M Jenkins et al.   BMC GENOMICS

Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

(2015) Murukarthick Jayakodi et al.   BMC GENOMICS

Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae

(2015) Setareh Mohammadin et al.   BMC PLANT BIOLOGY

Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

(2015) Yafei Yin et al.   Cell Stem Cell

Identification of Novel Long Noncoding RNAs Underlying Vertebrate Cardiovascular Development

(2015) L. Kurian et al.   CIRCULATION

A Long Non-coding RNA, LncMyoD, Regulates Skeletal Muscle Differentiation by Blocking IMP2-Mediated mRNA Translation

(2015) Chenguang Gong et al.   DEVELOPMENTAL CELL

Reverse Genetic Screening Reveals Poor Correlation between Morpholino-Induced and Mutant Phenotypes in Zebrafish

(2015) Fatma O. Kok et al.   DEVELOPMENTAL CELL

Regulation of the ESC transcriptome by nuclear long noncoding RNAs

(2015) Jan H. Bergmann et al.   GENOME RESEARCH

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

(2015) Jennifer Y. Tan et al.   GENOME RESEARCH

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis

(2015) Samir Ounzain et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Human Long Noncoding RNAs Are Substantially Less Folded than Messenger RNAs

(2015) Jian-Rong Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity

(2015) Federico Gaiti et al.   MOLECULAR BIOLOGY AND EVOLUTION

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

(2015) Jens Durruthy-Durruthy et al.   NATURE GENETICS

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypiumspp.)

(2015) Maojun Wang et al.   NEW PHYTOLOGIST

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits

(2015) Huan Wang et al.   PLANT JOURNAL

Human pluripotent stem cell-derived neural constructs for predicting neural toxicity

(2015) Michael P. Schwartz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcispongeSycon ciliatum

(2015) Jon Bråte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci

(2015) Wilfried Haerty et al.   RNA

Evolutionary annotation of conserved long non-coding RNAs in major mammalian species

(2015) DeChao Bu et al.   Science China-Life Sciences

The conservation and signatures of lincRNAs in Marek’s disease of chicken

(2015) Yanghua He et al.   Scientific Reports

The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2 Expression

(2015) Wei Jiang 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

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

(2015) Alexander Kanitz et al.   GENOME BIOLOGY

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Identification of long non-coding RNAs in insects genomes

(2015) Fabrice Legeai et al.   Current Opinion in Insect Science

Conservation and Losses of Non-Coding RNAs in Avian Genomes

(2015) Paul P. Gardner et al.   PLoS One

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

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

(2014) S. Washietl et al.   GENOME RESEARCH

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse

(2014) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light

(2014) Y. Wang 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

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

New Gene Evolution: Little Did We Know

(2013) Manyuan Long et al.   Annual Review of Genetics

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Gene regulation by the act of long non-coding RNA transcription

(2013) Aleksandra E Kornienko et al.   BMC BIOLOGY

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

(2013) Vincent C. Auyeung et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

(2013) H. Maamar et al.   GENES & DEVELOPMENT

Evolutionarily conserved long intergenic non-coding RNAs in the eye

(2013) Debarshi Mustafi et al.   HUMAN MOLECULAR GENETICS

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

(2013) Ibrahim Avsar Ilik et al.   MOLECULAR CELL

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Widespread purifying selection on RNA structure in mammals

(2013) Martin A. Smith et al.   NUCLEIC ACIDS RESEARCH

Bidirectional Promoters as Important Drivers for the Emergence of Species-Specific Transcripts

(2013) Valer Gotea et al.   PLoS One

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression

(2013) Lingjie Li et al.   Cell Reports

DUX4 Binding to Retroelements Creates Promoters That Are Active in FSHD Muscle and Testis

(2013) Janet M. Young 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

Mutations within lncRNAs are effectively selected against in fruitfly but not in human

(2013) Wilfried Haerty et al.   GENOME BIOLOGY

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes

(2012) Ignasi Morán et al.   Cell Metabolism

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

(2012) J. E. Wilusz et al.   GENES & DEVELOPMENT

Activity-Dependent Human Brain Coding/Noncoding Gene Regulatory Networks

(2012) L. Lipovich et al.   GENETICS

Long noncoding RNAs in C. elegans

(2012) J.-W. Nam 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

Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation

(2012) Jennifer Grant et al.   NATURE

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

(2012) Claudia Carrieri et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

Isoform Diversity and Regulation in Peripheral and Central Neurons Revealed through RNA-Seq

(2012) Jessica K. Lerch et al.   PLoS One

Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing

(2012) P. A. Latos et al.   SCIENCE

Conservation of a Triple-Helix-Forming RNA Stability Element in Noncoding and Genomic RNAs of Diverse Viruses

(2012) Kazimierz T. Tycowski et al.   Cell Reports

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

Origin and evolution of the long non-coding genes in the X-inactivation center

(2011) Antonio Romito et al.   BIOCHIMIE

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

(2011) Igor Ulitsky et al.   CELL

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

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

Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

(2011) David Managadze et al.   Genome Biology and Evolution

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

(2011) Sandra Ruf et al.   NATURE GENETICS

Evolution of microRNA diversity and regulation in animals

(2011) Eugene Berezikov   NATURE REVIEWS GENETICS

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

Structural and Functional Differences in the Long Non-Coding RNA Hotair in Mouse and Human

(2011) Patrick Schorderet et al.   PLoS Genetics

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

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

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

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

(2009) Mitchell Guttman et al.   NATURE

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo prediction of structured RNAs from genomic sequences

(2009) Jan Gorodkin et al.   TRENDS IN BIOTECHNOLOGY

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

Regulation of Histone H4 Lys16 Acetylation by Predicted Alternative Secondary Structures in roX Noncoding RNAs

(2008) S.-W. Park et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE