Cellular functions of long noncoding RNAs

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

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance

(2018) Assaf C. Bester et al.   CELL

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   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

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

(2018) Benjamin Kleaveland et al.   CELL

High‐throughput identification of RNA nuclear enrichment sequences

(2018) Chinmay J Shukla et al.   EMBO JOURNAL

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

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

(2018) Qinyu Sun et al.   TRENDS IN GENETICS

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

Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria

(2018) Yang Wang et al.   NATURE CELL BIOLOGY

Neat1 is a p53-inducible lincRNA essential for transformation suppression

(2017) Stephano S. Mello et al.   GENES & DEVELOPMENT

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

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

(2017) Julia Joung et al.   NATURE

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

The X chromosome in space

(2017) Teddy Jégu et al.   NATURE REVIEWS GENETICS

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture

(2017) K. M. Creamer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1)

(2017) Hongjae Sunwoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional dissection of NEAT1 using genome editing reveals substantial localization of the NEAT1_1 isoform outside paraspeckles

(2017) Ruohan Li et al.   RNA

PCGF3/5–PRC1 initiates Polycomb recruitment in X chromosome inactivation

(2017) Mafalda Almeida et al.   SCIENCE

Comment on “Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing”

(2017) Chen-Yu Wang et al.   SCIENCE

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies

(2016) Takeshi Chujo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Ribonucleic Complex HuR-MALAT1 Represses CD133 Expression and Suppresses Epithelial-Mesenchymal Transition in Breast Cancer

(2016) E. Latorre et al.   CANCER RESEARCH

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

(2016) Pushkar Malakar et al.   CANCER RESEARCH

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

(2016) Sungyul Lee et al.   CELL

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

(2016) Marta Melé et al.   GENOME RESEARCH

The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL

(2016) Taro Mannen et al.   JOURNAL OF CELL BIOLOGY

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

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

(2016) Kelly M. Anderson et al.   NATURE

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

(2016) Jesse M. Engreitz et al.   NATURE

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

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

(2016) Jianle Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) B. R. Nelson et al.   SCIENCE

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

(2016) C.-K. Chen et al.   SCIENCE

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu 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

Hotair Is Dispensible for Mouse Development

(2016) Ana Rita Amândio et al.   PLoS Genetics

Circadian RNA expression elicited by 3’-UTR IRAlu-paraspeckle associated elements

(2016) Manon Torres et al.   eLife

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

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Alu element-containing RNAs maintain nucleolar structure and function

(2015) M. Caudron-Herger et al.   EMBO JOURNAL

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus

(2015) Shi-Bin Hu et al.   GENES & DEVELOPMENT

Differentiation of mammary tumors and reduction in metastasis uponMalat1lncRNA loss

(2015) Gayatri Arun et al.   GENES & DEVELOPMENT

Toward a Consensus on the Binding Specificity and Promiscuity of PRC2 for RNA

(2015) Chen Davidovich 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

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

(2015) Colleen A. McHugh et al.   NATURE

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells

(2015) Hongjae Sunwoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

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

(2015) A. Minajigi et al.   SCIENCE

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

Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex

(2014) Q Ji et al.   BRITISH JOURNAL OF CANCER

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

(2014) Jesse M. Engreitz et al.   CELL

Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes

(2014) Lisa L. Hall 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

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

A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

(2014) B. Zhang et al.   MOLECULAR AND CELLULAR BIOLOGY

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

(2014) Katsutoshi Imamura 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

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

(2014) Eliezer Calo et al.   NATURE

A long noncoding RNA protects the heart from pathological hypertrophy

(2014) Pei Han et al.   NATURE

PVT1 dependence in cancer with MYC copy-number increase

(2014) Yuen-Yi Tseng et al.   NATURE

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

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

Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy

(2014) Andrea Cerase et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Laura Standaert et al.   RNA

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

(2014) P. Wang et al.   SCIENCE

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

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

Transcriptome-wide identification of RNA binding sites by CLIP-seq

(2013) Valentine Murigneux et al.   METHODS

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

(2013) Tetsuro Hirose et al.   MOLECULAR BIOLOGY OF THE CELL

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

(2013) Matthew D. Simon et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam 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

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini 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

Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression

(2013) Lingjie Li et al.   Cell Reports

Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles

(2012) Takao Naganuma et al.   EMBO JOURNAL

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 Noncoding RNAs with snoRNA Ends

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

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon et al.   MOLECULAR CELL

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

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

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

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

(2011) Leonardo Salmena 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

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

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

Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases

(2011) T. Gutschner 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

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

The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies

(2010) Sylvie Souquere et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

Roles of Puf proteins in mRNA degradation and translation

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

Paraspeckles: nuclear bodies built on long noncoding RNA

(2009) Charles S. Bond et al.   JOURNAL OF CELL 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

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen 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

Alu element-mediated gene silencing

(2008) Ling-Ling Chen et al.   EMBO JOURNAL

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

Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock

(2008) Peter D. Mariner et al.   MOLECULAR CELL

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

(2008) J. Zhao et al.   SCIENCE