Technologies to probe functions and mechanisms of long noncoding RNAs

High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device

(2014) Kylan Szeto et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

The long non-coding RNA Paupar regulates the expression of both local and distal genes

(2014) K. W. Vance et al.   EMBO JOURNAL

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

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

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

(2014) Jason D Buenrostro et al.   NATURE BIOTECHNOLOGY

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

(2014) Jeffrey J Quinn et al.   NATURE BIOTECHNOLOGY

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)

(2014) Aleksandra Helwak et al.   Nature Protocols

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

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

A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase

(2014) Roman Martin et al.   RNA

Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome

(2014) D. Colak et al.   SCIENCE

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release

(2013) Wen Liu et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

A Prader–Willi locus lncRNA cloud modulates diurnal genes and energy expenditure

(2013) Weston T. Powell et al.   HUMAN MOLECULAR GENETICS

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

(2013) Valentine Murigneux et al.   METHODS

ATP-Dependent roX RNA Remodeling by the Helicase maleless Enables Specific Association of MSL Proteins

(2013) Sylvain Maenner et al.   MOLECULAR CELL

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

(2013) Ibrahim Avsar Ilik et al.   MOLECULAR CELL

The Long Noncoding RNA RMST Interacts with SOX2 to Regulate Neurogenesis

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

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

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

(2013) Matthew D. Simon et al.   NATURE

Translating dosage compensation to trisomy 21

(2013) Jun Jiang et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

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

(2013) Silvi Rouskin et al.   NATURE

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

(2013) Yue Wan et al.   Nature Protocols

A modular strategy for engineering orthogonal chimeric RNA transcription regulators

(2013) Melissa K. Takahashi et al.   NUCLEIC ACIDS RESEARCH

The long noncoding RNA THRIL regulates TNF  expression through its interaction with hnRNPL

(2013) Z. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Long noncoding RNAs: fresh perspectives into the RNA world

(2013) Lin Yang et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

(2012) Z. Ouyang et al.   GENOME RESEARCH

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

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

(2012) Markus Kretz et al.   NATURE

RNA SHAPE analysis in living cells

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

Systematic reconstruction of RNA functional motifs with high-throughput microfluidics

(2012) Lance Martin et al.   NATURE METHODS

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

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

Quantifying RNA–protein interactions in situ using modified-MTRIPs and proximity ligation

(2012) Jeenah Jung et al.   NUCLEIC ACIDS RESEARCH

Association of Argonaute proteins and microRNAs can occur after cell lysis

(2012) K. J. Riley et al.   RNA

The Yeast Rab GTPase Ypt1 Modulates Unfolded Protein Response Dynamics by Regulating the Stability of HAC1 RNA

(2012) Nikoleta G. Tsvetanova et al.   PLoS Genetics

KSHV PAN RNA Associates with Demethylases UTX and JMJD3 to Activate Lytic Replication through a Physical Interaction with the Virus Genome

(2012) Cyprian C. Rossetto et al.   PLoS Pathogens

Exploring RNA Structural Codes with SHAPE Chemistry

(2011) Kevin M. Weeks et al.   ACCOUNTS OF CHEMICAL RESEARCH

Fifty years of X-inactivation research

(2011) A.-V. Gendrel et al.   DEVELOPMENT

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

(2011) Ci Chu et al.   MOLECULAR CELL

The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity

(2011) Nicole A Rapicavoli et al.   Neural Development

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

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

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

Epigenetic Licensing of Germline Gene Expression by Maternal RNA in C. elegans

(2011) C. L. Johnson et al.   SCIENCE

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

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling

(2009) Shaohui Hu et al.   CELL

Purification of Proteins Associated with Specific Genomic Loci

(2009) Jérôme Déjardin et al.   CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS