The functions of long noncoding RNAs in development and stem cells

Insight into lncRNA biology using hybridization capture analyses

(2016) Matthew D. Simon   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

Long Noncoding RNAs in Cancer Pathways

(2016) Adam M. Schmitt et al.   CANCER CELL

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

(2016) Sungyul Lee et al.   CELL

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

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

A Role for the Long Noncoding RNA SENCR in Commitment and Function of Endothelial Cells

(2016) Mounia Boulberdaa et al.   MOLECULAR THERAPY

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

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

Long noncoding RNAs in kidney and cardiovascular diseases

(2016) Johan M. Lorenzen et al.   Nature Reviews Nephrology

Effective knockdown ofDrosophilalong non-coding RNAs by CRISPR interference

(2016) Sanjay Ghosh et al.   NUCLEIC ACIDS RESEARCH

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

(2016) Joana Carlevaro-Fita et al.   RNA

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

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

(2016) Ailone Tichon et al.   Nature Communications

HoxBlinc RNA Recruits Set1/MLL Complexes to Activate Hox Gene Expression Patterns and Mesoderm Lineage Development

(2016) Changwang Deng et al.   Cell Reports

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

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

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

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

Differentiation of mammary tumors and reduction in metastasis uponMalat1lncRNA loss

(2015) Gayatri Arun et al.   GENES & DEVELOPMENT

Rap and chirp about X inactivation

(2015) Anna Roth et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

The emerging role of lncRNAs in cancer

(2015) Maite Huarte   NATURE MEDICINE

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner et al.   NATURE METHODS

Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation

(2015) Antonia A. Dominguez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides

(2015) Kim A. Lennox et al.   NUCLEIC ACIDS RESEARCH

Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain

(2015) Loyal A. Goff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

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

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

Long Noncoding RNAs: A New Regulatory Code in Metabolic Control

(2015) Xu-Yun Zhao et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs

(2015) Ka-Man Venus Lai et al.   PLoS One

Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation

(2014) Anne-Valerie Gendrel et al.   Annual Review of Cell and Developmental Biology

HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

(2014) Aliaksandr A Yarmishyn et al.   BMC GENOMICS

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Disruption ofVisc-2, a Brain-Expressed Conserved Long Noncoding RNA, Does Not Elicit an Overt Anatomical or Behavioral Phenotype

(2014) Peter L. Oliver et al.   CEREBRAL CORTEX

Long Noncoding RNA MALAT1 Regulates Endothelial Cell Function and Vessel Growth

(2014) Katharina M. Michalik et al.   CIRCULATION RESEARCH

The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice

(2014) S. Nakagawa et al.   DEVELOPMENT

Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development

(2014) M. J. Herriges et al.   GENES & DEVELOPMENT

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

(2014) S. Washietl et al.   GENOME RESEARCH

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

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

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification

(2014) Jeffrey J Quinn et al.   NATURE BIOTECHNOLOGY

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

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

Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish

(2014) Kriti Kaushik et al.   PLoS One

The long noncoding RNA Neat1 is required for mammary gland development and lactation

(2014) Laura Standaert et al.   RNA

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

(2014) A. Pauli et al.   SCIENCE

Physiological roles of long noncoding RNAs: insight from knockout mice

(2014) Lingjie Li et al.   TRENDS IN CELL BIOLOGY

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

(2014) Aurélie Kapusta et al.   TRENDS IN GENETICS

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

(2014) Yul W Yang et al.   eLife

p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-κB complexes

(2014) Michal Krawczyk et al.   eLife

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

(2014) Sebastiaan van Heesch et al.   GENOME BIOLOGY

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

Xist RNA Is a Potent Suppressor of Hematologic Cancer in Mice

(2013) Eda Yildirim et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

Evf2 (Dlx6as) lncRNA regulates ultraconserved enhancer methylation and the differential transcriptional control of adjacent genes

(2013) E. G. Berghoff et al.   DEVELOPMENT

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

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

Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment

(2013) Julieta Aprea et al.   EMBO JOURNAL

Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1)

(2013) Monika Hämmerle et al.   HEPATOLOGY

MALAT1 — a paradigm for long noncoding RNA function in cancer

(2013) Tony Gutschner et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

The Long Noncoding RNA RMST Interacts with SOX2 to Regulate Neurogenesis

(2013) Shi-Yan Ng et al.   MOLECULAR CELL

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

(2013) Sebastian Memczak et al.   NATURE

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1

(2013) P. Monnier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNAs regulate adipogenesis

(2013) Lei Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noncoding RNA and Polycomb recruitment

(2013) N. Brockdorff   RNA

Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression

(2013) Lingjie Li et al.   Cell Reports

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

(2013) Aurélie Kapusta et al.   PLoS Genetics

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

(2013) Oskar Marín-Béjar et al.   GENOME BIOLOGY

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

(2012) M. Kretz et al.   GENES & DEVELOPMENT

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

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

(2012) Claudia Carrieri et al.   NATURE

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Loss of the abundant nuclear non-coding RNAMALAT1is compatible with life and development

(2012) Moritz Eißmann et al.   RNA Biology

Malat1 is not an essential component of nuclear speckles in mice

(2012) S. Nakagawa et al.   RNA

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

(2012) P. A. Latos et al.   SCIENCE

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

(2012) Bin Zhang et al.   Cell Reports

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

(2012) David Kelley et al.   GENOME BIOLOGY

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

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

(2011) Shinichi Nakagawa et al.   JOURNAL OF CELL BIOLOGY

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

(2011) Chenguang Gong et al.   NATURE

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

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

(2011) Sandra Ruf et al.   NATURE GENETICS

Non-coding RNAs as regulators of embryogenesis

(2011) Andrea Pauli et al.   NATURE REVIEWS GENETICS

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

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

(2011) Patrick Schorderet et al.   PLoS Genetics

Epigenetic control of Hox genes during neurogenesis, development, and disease

(2010) Benjamin A. Barber et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

RNA traffic control of chromatin complexes

(2010) Magdalena J Koziol et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression

(2010) Delphine Bernard et al.   EMBO JOURNAL

Human LSD2/KDM1b/AOF1 Regulates Gene Transcription by Modulating Intragenic H3K4me2 Methylation

(2010) Rui Fang et al.   MOLECULAR CELL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Molecular Interplay of the Noncoding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a

(2010) Kyoko L. Yap et al.   MOLECULAR CELL

Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 INK4B tumor suppressor gene

(2010) Y Kotake et al.   ONCOGENE

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

H19 acts as a trans regulator of the imprinted gene network controlling growth in mice

(2009) A. Gabory et al.   DEVELOPMENT

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

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

(2009) Mitchell Guttman et al.   NATURE

Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry

(2009) Allison M Bond et al.   NATURE NEUROSCIENCE

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

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

Gene Regulation by Transcription Factors and MicroRNAs

(2008) O. Hobert   SCIENCE

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE

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

(2008) J. Zhao et al.   SCIENCE