Long non-coding RNAs and transposable elements: A functional relationship

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

(2020) Alessandro Bonetti et al.   Nature Communications

LEADeR role of miR-205 host gene as long noncoding RNA in prostate basal cell differentiation

(2019) Valentina Profumo et al.   Nature Communications

RBPSponge: genome-wide identification of lncRNAs that sponge RBPs

(2019) Saber HafezQorani et al.   BIOINFORMATICS

BACE1-AS prevents BACE1 mRNA degradation through the sequestration of BACE1-targeting miRNAs

(2019) Tao Zeng et al.   JOURNAL OF CHEMICAL NEUROANATOMY

Chromatin-associated RNAs as facilitators of functional genomic interactions

(2019) Xiao Li et al.   NATURE REVIEWS GENETICS

The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs

(2019) Francesca Fasolo et al.   FASEB JOURNAL

Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels

(2019) Xiaopei Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mapping RNA–chromatin interactions by sequencing with iMARGI

(2019) Weixin Wu et al.   Nature Protocols

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

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

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Splicing regulation by long noncoding RNAs

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

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

(2018) Martin Raden et al.   NUCLEIC ACIDS RESEARCH

Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

(2018) Qinyu Sun et al.   TRENDS IN GENETICS

Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function

(2018) Yifei Miao et al.   Nature Communications

Cytoplasmic functions of long noncoding RNAs

(2018) Ji Heon Noh et al.   Wiley Interdisciplinary Reviews-RNA

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

(2018) Jason C Bell et al.   eLife

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

(2018) Takafumi Chishima et al.   Genes

piRNAs and PIWI proteins: regulators of gene expression in development and stem cells

(2018) Patricia Rojas-Ríos et al.   DEVELOPMENT

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

(2018) Yoav Lubelsky et al.   NATURE

COMRADES determines in vivo RNA structures and interactions

(2018) Omer Ziv et al.   NATURE METHODS

Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs

(2018) Joana Carlevaro-Fita et al.   GENOME RESEARCH

Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints

(2017) Corinne N. Simonti et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Greta Pintacuda et al.   MOLECULAR CELL

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

ALU ternative Regulation for Gene Expression

(2017) Ling-Ling Chen et al.   TRENDS IN CELL BIOLOGY

Genome-wide characterization of human L1 antisense promoter-driven transcripts

(2016) Steven W. Criscione et al.   BMC GENOMICS

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

(2016) Zhipeng Lu et al.   CELL

Unlinking an lncRNA from Its Associated cis Element

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

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

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

(2016) Jesse M. Engreitz et al.   NATURE

LNCediting: a database for functional effects of RNA editing in lncRNAs

(2016) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

LncRNAOIP5-AS1/cyranosponges RNA-binding protein HuR

(2016) Jiyoung Kim et al.   NUCLEIC ACIDS RESEARCH

Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

(2016) Tri C. Nguyen 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

ATtRACT—a database of RNA-binding proteins and associated motifs

(2016) Girolamo Giudice et al.   Database-The Journal of Biological Databases and Curation

Synthetic long non-coding RNAs [SINEUPs] rescue defective gene expression in vivo

(2016) Alessia Indrieri et al.   Scientific Reports

Identification of antisense long noncoding RNAs that function as SINEUPs in human cells

(2016) Aleks Schein et al.   Scientific Reports

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

(2015) Bodu Liu et al.   CANCER CELL

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

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

(2015) Colleen A. McHugh et al.   NATURE

Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome)

(2015) Laura Patrucco et al.   RNA Biology

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

(2014) Jesse M. Engreitz et al.   CELL

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

TE composition of human long noncoding RNAs and their expression patterns in human tissues

(2014) Donghee Kang et al.   Genes & Genomics

Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline

(2014) Toshiaki Watanabe et al.   GENOME RESEARCH

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

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

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

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

(2014) R. Johnson et al.   RNA

Pseudogene OCT4-pg4 functions as a natural micro RNA sponge to regulate OCT4 expression by competing for miR-145 in hepatocellular carcinoma

(2013) Lei Wang et al.   CARCINOGENESIS

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

Control of myogenesis by rodent SINE-containing lncRNAs

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

The Intertwining of Transposable Elements and Non-Coding RNAs

(2013) Michael Hadjiargyrou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Reciprocal Regulation of HIF-1α and LincRNA-p21 Modulates the Warburg Effect

(2013) Fan Yang et al.   MOLECULAR CELL

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

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

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs

(2013) Deeksha Bhartiya et al.   Database-The Journal of Biological Databases and Curation

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

(2013) Aurélie Kapusta et al.   PLoS Genetics

Long non-coding RNAgadd7interacts with TDP-43 and regulatesCdk6mRNA decay

(2012) Xuefeng Liu et al.   EMBO JOURNAL

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon 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

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy

(2012) F. Cartault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) P. A. Latos et al.   SCIENCE

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

(2012) David Kelley et al.   GENOME BIOLOGY

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

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

(2011) Chenguang Gong et al.   NATURE

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

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

Noncoding RNA Gas5 Is a Growth Arrest- and Starvation-Associated Repressor of the Glucocorticoid Receptor

(2010) T. Kino et al.   Science Signaling

Evidence for natural antisense transcript-mediated inhibition of microRNA function

(2010) Mohammad Ali Faghihi et al.   GENOME BIOLOGY

Alu element-mediated gene silencing

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

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

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

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