Mechanisms of long noncoding RNA function in development and disease

Long noncoding RNAs: Lessons from genomic imprinting

(2016) Chandrasekhar Kanduri   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Review toward all RNA structures, concisely

(2015) Kevin M. Weeks   BIOPOLYMERS

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

(2015) Xiaohui Yan et al.   CANCER CELL

A Cytoplasmic NF-κB Interacting Long Noncoding RNA Blocks IκB Phosphorylation and Suppresses Breast Cancer Metastasis

(2015) Bodu Liu et al.   CANCER CELL

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

(2015) Douglas M. Anderson et al.   CELL

The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling

(2015) Yanying Wang et al.   Cell Stem Cell

The Long Noncoding RNA Pnky Regulates Neuronal Differentiation of Embryonic and Postnatal Neural Stem Cells

(2015) Alexander D. Ramos et al.   Cell Stem 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

Gene activation-associated long noncoding RNAs function in mouse preimplantation development

(2015) N. Hamazaki et al.   DEVELOPMENT

Evf2lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling

(2015) Ivelisse Cajigas et al.   DEVELOPMENT

A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation

(2015) Vanessa Lopez-Pajares et al.   DEVELOPMENTAL CELL

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

(2015) Chenguang Gong et al.   DEVELOPMENTAL CELL

The steroid receptor RNA activator protein (SRAP) controls cancer cell migration/motility

(2015) Yi Yan et al.   FEBS LETTERS

Differentiation of mammary tumors and reduction in metastasis uponMalat1lncRNA loss

(2015) Gayatri Arun et al.   GENES & DEVELOPMENT

Regulation of the ESC transcriptome by nuclear long noncoding RNAs

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

Linking RNA biology to lncRNAs

(2015) Loyal A. Goff et al.   GENOME RESEARCH

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

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

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

(2015) Anne Nitsche et al.   RNA

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

(2015) Wilfried Haerty et al.   RNA

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Long noncoding RNAs in organogenesis: making the difference

(2015) Phillip Grote et al.   TRENDS IN GENETICS

A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture

(2015) Jacek Krol et al.   Nature Communications

The lncRNA MIR31HG regulates p16INK4A expression to modulate senescence

(2015) Marta Montes et al.   Nature Communications

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

(2015) Tanmoy Mondal et al.   Nature Communications

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes

(2015) Michael S. Werner et al.   Cell Reports

Long Noncoding RNA Ceruloplasmin Promotes Cancer Growth by Altering Glycolysis

(2015) Rajesha Rupaimoole et al.   Cell Reports

The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2 Expression

(2015) Wei Jiang et al.   Cell Reports

PARTICLE, a Triplex-Forming Long ncRNA, Regulates Locus-Specific Methylation in Response to Low-Dose Irradiation

(2015) Valerie Bríd O’Leary et al.   Cell Reports

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

(2015) Fan Yang et al.   GENOME BIOLOGY

The lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer

(2015) John R. Prensner et al.   Oncotarget

The Risk-Associated Long Noncoding RNA NBAT-1 Controls Neuroblastoma Progression by Regulating Cell Proliferation and Neuronal Differentiation

(2014) Gaurav Kumar Pandey et al.   CANCER CELL

A Functional Genomic Approach Identifies FAL1 as an Oncogenic Long Noncoding RNA that Associates with BMI1 and Represses p21 Expression in Cancer

(2014) Xiaowen Hu et al.   CANCER CELL

lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals

(2014) Zhen Xing et al.   CELL

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

(2014) Thomas Trimarchi 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

LincRNA-p21 Regulates Neointima Formation, Vascular Smooth Muscle Cell Proliferation, Apoptosis, and Atherosclerosis by Enhancing p53 Activity

(2014) Gengze Wu et al.   CIRCULATION

Circulating Long Noncoding RNA, LIPCAR, Predicts Survival in Patients With Heart Failure

(2014) Regalla Kumarswamy et al.   CIRCULATION RESEARCH

Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs

(2014) S. Ounzain et al.   EUROPEAN HEART JOURNAL

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

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

The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration

(2014) B. K. Dey et al.   GENES & DEVELOPMENT

Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease

(2014) Samir Ounzain et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome

(2014) Simão Teixeira da Rocha et al.   MOLECULAR CELL

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

(2014) Nadya Dimitrova et al.   MOLECULAR CELL

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

(2014) Nianwei Lin et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

A long noncoding RNA protects the heart from pathological hypertrophy

(2014) Pei Han et al.   NATURE

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

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

Epigenetic coordination of embryonic heart transcription by dynamically regulated long noncoding RNAs

(2014) S. J. Matkovich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) A. Pauli et al.   SCIENCE

The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation

(2014) P. Wang et al.   SCIENCE

The four dimensions of noncoding RNA conservation

(2014) Sven Diederichs   TRENDS IN GENETICS

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

(2014) Yolanda Sánchez et al.   Nature Communications

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

The long non-coding RNA Dali is an epigenetic regulator of neural differentiation

(2014) Vladislava Chalei et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera 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

Downregulated LncRNA-ANCR promotes osteoblast differentiation by targeting EZH2 and regulating Runx2 expression

(2013) Lin Zhu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Jpx RNA Activates Xist by Evicting CTCF

(2013) Sha Sun et al.   CELL

The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-γ Locus

(2013) J. Antonio Gomez et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista 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

Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo

(2013) Alexander D. Ramos et al.   Cell Stem Cell

Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway

(2013) Guohui Wan et al.   CELLULAR SIGNALLING

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

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

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

Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

(2013) Irina V. Novikova et al.   JOURNAL OF MOLECULAR BIOLOGY

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

The Long Noncoding RNA RMST Interacts with SOX2 to Regulate Neurogenesis

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

The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing

(2013) G Barry et al.   MOLECULAR PSYCHIATRY

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

(2013) Liuqing Yang et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

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

(2013) Sebastian Memczak et al.   NATURE

The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex

(2013) John R Prensner et al.   NATURE GENETICS

Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity

(2013) Eleanor Wheeler et al.   NATURE GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

(2013) Zhou Du et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The long non-coding RNAFendrrlinks epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis

(2013) Phillip Grote et al.   RNA Biology

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

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

(2013) Martin Sauvageau et al.   eLife

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

(2013) Nicole A Rapicavoli et al.   eLife

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

(2013) Alayne L Brunner et al.   GENOME BIOLOGY

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

(2013) Oskar Marín-Béjar 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

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells

(2012) T. Gutschner et al.   CANCER RESEARCH

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

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

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai 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

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz 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

Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all–iPS cell mice from terminally differentiated B cells

(2012) Matthias Stadtfeld et al.   NATURE GENETICS

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

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

(2011) Igor Ulitsky et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Long non-coding RNAs and enhancers

(2011) Ulf Andersson Ørom et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

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

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

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2011) Patrick Schorderet et al.   PLoS Genetics

The long noncoding RNA RNCR2 directs mouse retinal cell specification.

(2010) Nicole A Rapicavoli et al.   BMC DEVELOPMENTAL BIOLOGY

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

Activation of paternally expressed genes and perinatal death caused by deletion of the Gtl2 gene

(2010) Y. Zhou et al.   DEVELOPMENT

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

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

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

(2010) Jing Zhao et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

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

(2010) Rajnish A. Gupta et al.   NATURE

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

(2010) Axel Visel et al.   NATURE

Rmst Is a Novel Marker for the Mouse Ventral Mesencephalic Floor Plate and the Anterior Dorsal Midline Cells

(2010) Christopher W. Uhde et al.   PLoS One

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

(2009) X. Zhang et al.   BLOOD

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

WDR5, a complexed protein

(2009) Raymond C Trievel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

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

(2008) J. Zhao et al.   SCIENCE