Gene regulation by long non-coding RNAs and its biological functions

TINCR is not a non‐coding RNA but encodes a protein component of cornified epidermal keratinocytes

(2020) Leopold Eckhart et al.   EXPERIMENTAL DERMATOLOGY

Antisense-Mediated Transcript Knockdown Triggers Premature Transcription Termination

(2020) Jong-Sun Lee et al.   MOLECULAR CELL

Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination

(2020) Fan Lai et al.   MOLECULAR CELL

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA

(2020) Federico Ariel et al.   MOLECULAR CELL

Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6.

(2020) Michael Heskett et al.   RNA

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

(2020) Alessandro Bonetti et al.   Nature Communications

A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions

(2020) Elena Grossi et al.   Nature Communications

Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells

(2020) Chun-Jie Guo et al.   CELL

RIC-seq for global in situ profiling of RNA–RNA spatial interactions

(2020) Zhaokui Cai et al.   NATURE

U1 snRNP regulates chromatin retention of noncoding RNAs

(2020) Yafei Yin et al.   NATURE

RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2

(2020) Célia Alecki et al.   Nature Communications

Gene Architecture and Sequence Composition Underpin Selective Dependency of Nuclear Export of Long RNAs on NXF1 and the TREX Complex

(2020) Binyamin Zuckerman et al.   MOLECULAR CELL

RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells

(2020) Yicheng Long et al.   NATURE GENETICS

Antisense Oligonucleotides: An Emerging Area in Drug Discovery and Development

(2020) Karishma Dhuri et al.   Journal of Clinical Medicine

Long non-coding RNA TINCR as potential biomarker and therapeutic target for cancer

(2020) Uttam Sharma et al.   LIFE SCIENCES

A protein assembly mediates Xist localization and gene silencing

(2020) Amy Pandya-Jones et al.   NATURE

Long Non-coding RNAs: At the Heart of Cardiac Dysfunction?

(2019) Lisa Hobuß et al.   Frontiers in Physiology

lncRNA KHPS1 Activates a Poised Enhancer by Triplex-Dependent Recruitment of Epigenomic Regulators

(2019) Alena Blank-Giwojna et al.   Cell Reports

Predictive models of subcellular localization of long RNAs

(2019) Binyamin Zuckerman et al.   RNA

Nucleosomes Stabilize ssRNA-dsDNA Triple Helices in Human Cells

(2019) Rodrigo Maldonado et al.   MOLECULAR CELL

Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

(2019) David Colognori et al.   MOLECULAR CELL

Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening

(2019) Roberta Esposito et al.   CANCER CELL

LncRNA FIRRE is activated by MYC and promotes the development of diffuse large B-cell lymphoma via Wnt/β-catenin signaling pathway

(2019) Xue Shi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Function and Mechanism of Long Noncoding RNAs in Adipocyte Biology

(2019) Lei Sun et al.   DIABETES

HiChIRP reveals RNA-associated chromosome conformation

(2019) Maxwell R. Mumbach et al.   NATURE METHODS

Nuclear retention element recruits U1 snRNP components to restrain spliced lncRNAs in the nucleus

(2019) Sikandar Azam et al.   RNA Biology

PUMILIO hyperactivity drives premature aging of Norad-deficient mice

(2019) Florian Kopp et al.   eLife

The functions and oncogenic roles of CCAT1 in human cancer

(2019) Zheng Liu et al.   BIOMEDICINE & PHARMACOTHERAPY

The lncRNA Hand2os1/Uph locus orchestrates heart development through regulation of precise expression of Hand2

(2019) Xue Han et al.   DEVELOPMENT

lncRNA-Induced Spread of Polycomb Controlled by Genome Architecture, RNA Abundance, and CpG Island DNA

(2019) Megan D. Schertzer et al.   MOLECULAR CELL

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development

(2019) Nicole Ritter et al.   DEVELOPMENTAL CELL

Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway

(2019) Tina Uroda et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

Lnc RNA ‐dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

(2019) Kensuke Ninomiya et al.   EMBO JOURNAL

R-Loops Promote Antisense Transcription across the Mammalian Genome

(2019) Sue Mei Tan-Wong et al.   MOLECULAR CELL

Regulation of gene expression by cis-acting long non-coding RNAs

(2019) Noa Gil et al.   NATURE REVIEWS GENETICS

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

(2019) Jordan P. Lewandowski et al.   Nature Communications

Importance of Long Non-coding RNAs in the Development and Disease of Skeletal Muscle and Cardiovascular Lineages

(2019) Sweta Sweta et al.   Frontiers in Cell and Developmental Biology

HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice

(2019) Huacheng Luo et al.   CANCER CELL

Plasma long non-coding RNA BACE1 as a novel biomarker for diagnosis of Alzheimer disease

(2018) Liang Feng et al.   BMC Neurology

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

(2018) Zehua Wang et al.   CANCER CELL

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

High‐throughput identification of RNA nuclear enrichment sequences

(2018) Chinmay J Shukla et al.   EMBO JOURNAL

SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA

(2018) Ailone Tichon et al.   GENES & DEVELOPMENT

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C

(2018) Philipp G. Maass et al.   MOLECULAR CELL

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

GUARDIN is a p53-responsive long non-coding RNA that is essential for genomic stability

(2018) Wang Lai Hu et al.   NATURE CELL BIOLOGY

Principles for targeting RNA with drug-like small molecules

(2018) Katherine Deigan Warner et al.   NATURE REVIEWS DRUG DISCOVERY

Towards a complete map of the human long non-coding RNA transcriptome

(2018) Barbara Uszczynska-Ratajczak et al.   NATURE REVIEWS GENETICS

Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture

(2018) Yizhu Lin et al.   NUCLEIC ACIDS RESEARCH

Splicing regulation by long noncoding RNAs

(2018) Natali Romero-Barrios et al.   NUCLEIC ACIDS RESEARCH

HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis

(2018) Wanju Jiao et al.   ONCOGENE

Identification of RNA-binding proteins in exosomes capable of interacting with different types of RNA: RBP-facilitated transport of RNAs into exosomes

(2018) Luisa Statello et al.   PLoS One

New and Prospective Roles for lncRNAs in Organelle Formation and Function

(2018) Henry M. Krause   TRENDS IN GENETICS

TERRA recruitment of polycomb to telomeres is essential for histone trymethylation marks at telomeric heterochromatin

(2018) Juan J. Montero et al.   Nature Communications

The effects of mitochondria-associated long noncoding RNAs in cancer mitochondria: New players in an old arena

(2018) Yijing Zhao et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

(2018) Mathias Munschauer et al.   NATURE

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

(2018) Yoav Lubelsky et al.   NATURE

Functional classification of long non-coding RNAs by k-mer content

(2018) Jessime M. Kirk et al.   NATURE GENETICS

NKILA lncRNA promotes tumor immune evasion by sensitizing T cells to activation-induced cell death

(2018) Di Huang et al.   NATURE IMMUNOLOGY

Stress-Induced Low Complexity RNA Activates Physiological Amyloidogenesis

(2018) Miling Wang et al.   Cell Reports

The Role of Long Noncoding RNAs in Central Nervous System and Neurodegenerative Diseases

(2018) Chang-Wei Wei et al.   Frontiers in Behavioral Neuroscience

ANRIL: A lncRNA at the CDKN2A/B Locus With Roles in Cancer and Metabolic Disease

(2018) Yahui Kong et al.   Frontiers in Endocrinology

Global transcriptional activity dynamics reveal functional enhancer RNAs

(2018) Yoon Jung Kim et al.   GENOME RESEARCH

Regulation of Neuroregeneration by Long Noncoding RNAs

(2018) Rotem Ben-Tov Perry et al.   MOLECULAR CELL

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival

(2018) Karen Yap et al.   MOLECULAR CELL

GADD45A binds R-loops and recruits TET1 to CpG island promoters

(2018) Khelifa Arab et al.   NATURE GENETICS

Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

(2018) Stephanie Fanucchi et al.   NATURE GENETICS

SAMMSON fosters cancer cell fitness by concertedly enhancing mitochondrial and cytosolic translation

(2018) Roberto Vendramin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers

(2018) Yue Gao et al.   NUCLEIC ACIDS RESEARCH

Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features

(2018) Brian L. Gudenas et al.   Scientific Reports

Divergent lncRNA GATA3-AS1 Regulates GATA3 Transcription in T-Helper 2 Cells

(2018) Hunter R. Gibbons et al.   Frontiers in Immunology

Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity

(2018) Noa Gil et al.   Cell Systems

Long Non-coding RNA NEAT1: A Novel Target for Diagnosis and Therapy in Human Tumors

(2018) Peixin Dong et al.   Frontiers in Genetics

Noncoding RNA activated by DNA damage (NORAD): Biologic function and mechanisms in human cancers

(2018) Zhi Yang et al.   CLINICA CHIMICA ACTA

L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing

(2017) Emily J. Platt et al.   JOURNAL OF CELL BIOLOGY

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

(2017) Jingyi Fei et al.   JOURNAL OF CELL SCIENCE

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

(2017) Greta Pintacuda et al.   MOLECULAR CELL

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks

(2017) Flavia Michelini et al.   NATURE CELL BIOLOGY

A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumour progression

(2017) Simon Grelet et al.   NATURE CELL BIOLOGY

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

(2017) Julien Lagarde et al.   NATURE GENETICS

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

lncRNA Functional Networks in Oligodendrocytes Reveal Stage-Specific Myelination Control by an lncOL1 /Suz12 Complex in the CNS

(2017) Danyang He et al.   NEURON

exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes

(2017) Shengli Li et al.   NUCLEIC ACIDS RESEARCH

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

Mechanistic insights in X-chromosome inactivation

(2017) Zhipeng Lu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Enhancer-Derived lncRNAs Regulate Genome Architecture: Fact or Fiction?

(2017) Stephanie Fanucchi et al.   TRENDS IN GENETICS

The Diversity of Long Noncoding RNAs and Their Generation

(2017) Huang Wu et al.   TRENDS IN GENETICS

cis -Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture

(2017) Jennifer Yihong Tan et al.   Cell Reports

HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development

(2017) Frédéric Laurent et al.   Cell Reports

Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3

(2017) Ritu Chaudhary et al.   eLife

Long non-coding RNA PVT1 and cancer

(2016) Ming Cui et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Long Noncoding RNA MALAT1 Promotes Hepatocellular Carcinoma Development by SRSF1 Upregulation and mTOR Activation

(2016) Pushkar Malakar et al.   CANCER RESEARCH

A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation

(2016) Maninjay K. Atianand et al.   CELL

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

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

New Xist -Interacting Proteins in X-Chromosome Inactivation

(2016) Hegias Mira-Bontenbal et al.   CURRENT BIOLOGY

Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication

(2016) Elena Carnero et al.   EMBO REPORTS

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

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

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

(2016) Marta Melé et al.   GENOME RESEARCH

Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization

(2016) Jason A. West et al.   JOURNAL OF CELL BIOLOGY

Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins

(2016) Huang Wu et al.   MOLECULAR CELL

LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56

(2016) Abhinav K. Jain et al.   MOLECULAR CELL

A Long Noncoding RNA Regulates Sister Chromatid Cohesion

(2016) Francesco P. Marchese et al.   MOLECULAR CELL

Unlinking an lncRNA from Its Associated cis Element

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

Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development

(2016) Kelly M. Anderson et al.   NATURE

Melanoma addiction to the long non-coding RNA SAMMSON

(2016) Eleonora Leucci et al.   NATURE

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan

(2016) Jonathan J. Kotzin et al.   NATURE

An inducible long noncoding RNA amplifies DNA damage signaling

(2016) Adam M Schmitt et al.   NATURE GENETICS

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2016) Joana Carlevaro-Fita et al.   RNA

A long noncoding RNA associated with susceptibility to celiac disease

(2016) A. Castellanos-Rubio et al.   SCIENCE

Function and evolution of local repeats in the Firre locus

(2016) Ezgi Hacisuleyman et al.   Nature Communications

Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes

(2016) Anirban Chakraborty et al.   Nature Communications

Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression

(2016) Stefanie Rosa et al.   Nature Communications

Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

(2016) Lovorka Stojic et al.   Nature Communications

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

(2016) Emily J. Hawkes et al.   Cell Reports

In Vivo Characterization of Linc-p21 Reveals Functional cis -Regulatory DNA Elements

(2016) Abigail F. Groff et al.   Cell Reports

Centromeric Transcription Regulates Aurora-B Localization and Activation

(2016) Michael D. Blower   Cell Reports

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

(2015) Bodu Liu et al.   CANCER CELL

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

Long Non-Coding RNAs Control Hematopoietic Stem Cell Function

(2015) Min Luo 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

A BRCA1-interacting lncRNA regulates homologous recombination

(2015) V. Sharma et al.   EMBO REPORTS

Long noncoding RNAs as a novel component of the Myc transcriptional network

(2015) Melanie Winkle et al.   FASEB JOURNAL

Differentiation of mammary tumors and reduction in metastasis uponMalat1lncRNA loss

(2015) Gayatri Arun et al.   GENES & DEVELOPMENT

Role of MYC-Regulated Long Noncoding RNAs in Cell Cycle Regulation and Tumorigenesis

(2015) Taewan Kim et al.   JNCI-Journal of the National Cancer Institute

Mitotic Transcription Installs Sgo1 at Centromeres to Coordinate Chromosome Segregation

(2015) Hong Liu et al.   MOLECULAR CELL

LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure

(2015) Anna Postepska-Igielska et al.   MOLECULAR CELL

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

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

(2015) Colleen A. McHugh et al.   NATURE

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

(2015) James A. Briggs et al.   NEURON

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

(2015) Raquel Boque-Sastre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA damage during the G0/G1 phase triggers RNA-templated, Cockayne syndrome B-dependent homologous recombination

(2015) Leizhen Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcript RNA supports precise repair of its own DNA gene

(2015) Havva Keskin et al.   RNA Biology

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Tissue-specific regulation of Igf2r/Airn imprinting during gastrulation

(2015) Chelsea Marcho et al.   Epigenetics & Chromatin

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation

(2015) Saori Tomita et al.   Nature Communications

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

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

ASAR15, A cis-Acting Locus that Controls Chromosome-Wide Replication Timing and Stability of Human Chromosome 15

(2015) Nathan Donley et al.   PLoS Genetics

Role of MYC-Regulated Long Noncoding RNAs in Cell Cycle Regulation and Tumorigenesis

(2015) Taewan Kim et al.   JNCI-Journal of the National Cancer Institute

MYC regulates the non-coding transcriptome

(2015) Jonathan R. Hart et al.   Oncotarget

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

(2014) Thomas Trimarchi et al.   CELL

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Molecular functions and cellular roles of the ChlR1 (DDX11) helicase defective in the rare cohesinopathy Warsaw breakage syndrome

(2014) Sanjay Kumar Bharti et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

X-chromosome inactivation in development and cancer

(2014) Ronan Chaligné et al.   FEBS LETTERS

Long Noncoding RNA TARID Directs Demethylation and Activation of the Tumor Suppressor TCF21 via GADD45A

(2014) Khelifa Arab 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

Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance

(2014) Rémy Denzler et al.   MOLECULAR CELL

Endogenous miRNA and Target Concentrations Determine Susceptibility to Potential ceRNA Competition

(2014) Andrew D. Bosson et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Transcript-RNA-templated DNA recombination and repair

(2014) Havva Keskin et al.   NATURE

PVT1 dependence in cancer with MYC copy-number increase

(2014) Yuen-Yi Tseng et al.   NATURE

A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element

(2014) Veronika A Herzog et al.   NATURE GENETICS

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

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

Negative regulation of the interferon response by an interferon-induced long non-coding RNA

(2014) Hiroto Kambara et al.   NUCLEIC ACIDS RESEARCH

AntisenseCOOLAIRmediates the coordinated switching of chromatin states atFLCduring vernalization

(2014) Tibor Csorba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5

(2014) T. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer

(2014) Dimple Chakravarty et al.   Nature Communications

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

(2014) Yolanda Sánchez et al.   Nature Communications

Functional characterization of the TERRA transcriptome at damaged telomeres

(2014) Antonio Porro et al.   Nature Communications

RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells

(2014) Rajika Arora et al.   Nature Communications

Lessons from Functional Analysis of Genome-Wide Association Studies

(2013) I. Sur et al.   CANCER RESEARCH

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

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

Silencing by the imprinted Airn macro lncRNA

(2013) Federica Santoro et al.   CELL CYCLE

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

Control of myogenesis by rodent SINE-containing lncRNAs

(2013) J. Wang et al.   GENES & DEVELOPMENT

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

(2013) H. Ling et al.   GENOME RESEARCH

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Translating dosage compensation to trisomy 21

(2013) Jun Jiang et al.   NATURE

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

(2013) Liuqing Yang et al.   NATURE

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence

(2013) Bettina Balk et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

(2013) Q. Sun et al.   SCIENCE

Asynchronous Replication, Mono-Allelic Expression, and Long Range Cis-Effects of ASAR6

(2013) Nathan Donley et al.   PLoS Genetics

The Intronic Long Noncoding RNA ANRASSF1 Recruits PRC2 to the RASSF1A Promoter, Reducing the Expression of RASSF1A and Increasing Cell Proliferation

(2013) Felipe C. Beckedorff 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

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

(2013) Martin Sauvageau et al.   eLife

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

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

(2012) J. E. Wilusz 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

MEG3 noncoding RNA: a tumor suppressor

(2012) Yunli Zhou et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

(2012) Vidisha Tripathi et al.   MOLECULAR BIOLOGY OF THE CELL

Long Noncoding RNAs with snoRNA Ends

(2012) Qing-Fei Yin et al.   MOLECULAR CELL

Immobilization of Proteins in the Nucleolus by Ribosomal Intergenic Spacer Noncoding RNA

(2012) Timothy E. Audas et al.   MOLECULAR CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

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

(2012) Markus Kretz et al.   NATURE

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

(2012) Claudia Carrieri et al.   NATURE

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

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

(2012) P. A. Latos et al.   SCIENCE

ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs

(2011) Liuqing Yang et al.   CELL

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

The Human Mitochondrial Transcriptome

(2011) Tim R. Mercer et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Transcription Regulation by the Noncoding RNA SRG1 Requires Spt2-Dependent Chromatin Deposition in the Wake of RNA Polymerase II

(2011) P. Thebault et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

(2011) Kevin C. Wang et al.   NATURE

TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA

(2011) Rachel Litman Flynn 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

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

RMRP Is a Non-Coding RNA Essential for Early Murine Development

(2011) Joseph Rosenbluh et al.   PLoS One

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins

(2011) O. Rackham et al.   RNA

The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization

(2011) M. M. Duszczyk et al.   RNA

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

Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1

(2010) F. Mohammad 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

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

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling

(2010) X. Peng et al.   mBio

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Roles of Puf proteins in mRNA degradation and translation

(2010) Melanie A. Miller et al.   Wiley Interdisciplinary Reviews-RNA

Evidence for natural antisense transcript-mediated inhibition of microRNA function

(2010) Mohammad Ali Faghihi et al.   GENOME BIOLOGY

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

TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres

(2009) Zhong Deng et al.   MOLECULAR CELL

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

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

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

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

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE