Platforms for Investigating LncRNA Functions

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

(2018) Assaf C. Bester et al.   CELL

Deciphering the roles of lncRNAs in breast development and disease

(2018) John Lalith Charles Richard et al.   Oncotarget

Measuring RNA structure transcriptome-wide with icSHAPE

(2017) Dalen Chan et al.   METHODS

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

(2017) Julia Joung et al.   NATURE

Nusinersen, an antisense oligonucleotide drug for spinal muscular atrophy

(2017) David R Corey   NATURE NEUROSCIENCE

A cautionary tale of sense-antisense gene pairs: independent regulation despite inverse correlation of expression

(2017) Ashish Goyal et al.   NUCLEIC ACIDS RESEARCH

Molecular Mechanisms of Antisense Oligonucleotides

(2017) Stanley T. Crooke   Nucleic Acid Therapeutics

Insight into lncRNA biology using hybridization capture analyses

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

Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering

(2016) Addison V. Wright et al.   CELL

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

(2016) Ryan A Flynn et al.   Nature Protocols

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs

(2016) Shangwei Ning et al.   NUCLEIC ACIDS RESEARCH

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

(2016) Ke-Ren Zhou et al.   NUCLEIC ACIDS RESEARCH

Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq

(2016) Cindo O. Nicholson et al.   RNA

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

(2016) S. John Liu et al.   SCIENCE

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

(2015) Daniel H. Kim et al.   Cell Stem Cell

Clinical and Preclinical Pharmacokinetics and Pharmacodynamics of Mipomersen (Kynamro®): A Second-Generation Antisense Oligonucleotide Inhibitor of Apolipoprotein B

(2015) Richard S. Geary et al.   CLINICAL PHARMACOKINETICS

Differentiation of mammary tumors and reduction in metastasis uponMalat1lncRNA loss

(2015) Gayatri Arun et al.   GENES & DEVELOPMENT

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

(2015) Colleen A. McHugh et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR 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

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP

(2015) Christian Hauer et al.   Nature Communications

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

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

(2014) Jesse M. Engreitz et al.   CELL

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

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

(2014) Luke A. Gilbert et al.   CELL

lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome

(2014) Wen-Ling Chan et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

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

Direct Binding of Ataxin-2 to Distinct Elements in 3′ UTRs Promotes mRNA Stability and Protein Expression

(2014) Moe Yokoshi et al.   MOLECULAR CELL

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2014) Jeffrey J Quinn et al.   NATURE BIOTECHNOLOGY

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Zooming in on lncRNA functions

(2014) Esther Lau   NATURE REVIEWS GENETICS

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

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

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression

(2014) Qinghua Jiang et al.   NUCLEIC ACIDS RESEARCH

An update on LNCipedia: a database for annotated human lncRNA sequences

(2014) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

(2014) Shaoli Das et al.   PLoS One

miRNA, siRNA, piRNA: Knowns of the unknown

(2014) Claudia Kutter et al.   RNA Biology

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L

(2014) Oliver Rossbach et al.   RNA Biology

Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9

(2014) Jinxiong Han et al.   RNA Biology

Long noncoding RNAs: an emerging link between gene regulation and nuclear organization

(2014) Sofia Quinodoz et al.   TRENDS IN CELL BIOLOGY

Long noncoding RNA HOTAIR involvement in cancer

(2014) Yansheng Wu et al.   TUMOR BIOLOGY

Long non-coding RNA UCA1 promotes breast tumor growth by suppression of p27 (Kip1)

(2014) J Huang et al.   Cell Death & Disease

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

(2014) Je-Hyun Yoon et al.   Nature Communications

RNAi Factors Are Present and Active in Human Cell Nuclei

(2014) Keith T. Gagnon et al.   Cell Reports

The Case for Junk DNA

(2014) Alexander F. Palazzo et al.   PLoS Genetics

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

Novel human lncRNA–disease association inference based on lncRNA expression profiles

(2013) Xing Chen et al.   BIOINFORMATICS

Gene regulation by the act of long non-coding RNA transcription

(2013) Aleksandra E Kornienko et al.   BMC BIOLOGY

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

(2013) Lei S. Qi et al.   CELL

A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility

(2013) Michael C. Bassik et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

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

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin 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

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

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

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

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

(2013) Yue Wan et al.   Nature Protocols

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

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

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes

(2012) Chenguang Gong et al.   METHODS

Genome-wide identification of miRNA targets by PAR-CLIP

(2012) Markus Hafner et al.   METHODS

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

FMRP targets distinct mRNA sequence elements to regulate protein expression

(2012) Manuel Ascano et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

Combined RNAi and localization for functionally dissecting long noncoding RNAs

(2012) Debojyoti Chakraborty et al.   NATURE METHODS

RNA therapeutics: beyond RNA interference and antisense oligonucleotides

(2012) Ryszard Kole et al.   NATURE REVIEWS DRUG DISCOVERY

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs

(2012) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Molecular Mechanisms of Long Noncoding RNAs

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

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

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

(2010) Jing Zhao et al.   MOLECULAR CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

GeneCards Version 3: the human gene integrator

(2010) M. Safran et al.   Database-The Journal of Biological Databases and Curation

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

NRED: a database of long noncoding RNA expression

(2008) Marcel E. Dinger et al.   NUCLEIC ACIDS RESEARCH

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