RNA structure probing uncovers RNA structure-dependent biological functions

Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

(2021) Lei Sun et al.   CELL RESEARCH

Keth-seq for transcriptome-wide RNA structure mapping

(2020) Xiaocheng Weng et al.   Nature Chemical Biology

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

Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques

(2020) Tina Uroda et al.   Nature Protocols

The expanding regulatory mechanisms and cellular functions of circular RNAs

(2020) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions

(2020) Christian Twittenhoff et al.   NUCLEIC ACIDS RESEARCH

The molecular structure of long non-coding RNAs: emerging patterns and functional implications

(2020) Isabel Chillón et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity

(2019) Chu-Xiao Liu et al.   CELL

Cellular functions of long noncoding RNAs

(2019) Run-Wen Yao et al.   NATURE CELL BIOLOGY

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus

(2019) Jörg Morf et al.   NATURE BIOTECHNOLOGY

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

(2019) Tina Uroda et al.   MOLECULAR CELL

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

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

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

mRNA structure determines specificity of a polyQ-driven phase separation

(2018) Erin M. Langdon et al.   SCIENCE

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A 360° view of circular RNAs: From biogenesis to functions

(2018) Jeremy E. Wilusz   Wiley Interdisciplinary Reviews-RNA

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

COMRADES determines in vivo RNA structures and interactions

(2018) Omer Ziv et al.   NATURE METHODS

High-throughput determination of RNA structures

(2018) Eric J. Strobel et al.   NATURE REVIEWS GENETICS

Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity

(2018) Pan Li et al.   Cell Host & Microbe

Higher-Order Organization Principles of Pre-translational mRNPs

(2018) Mihir Metkar et al.   MOLECULAR CELL

Assaying RNA structure with LASER-Seq

(2018) Boris Zinshteyn et al.   NUCLEIC ACIDS RESEARCH

Technique Development for Probing RNA Structure In Vivo and Genome-Wide

(2018) Philip C. Bevilacqua et al.   Cold Spring Harbor Perspectives in Biology

Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection

(2017) Xiang Li et al.   MOLECULAR CELL

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

Visualizing the secondary and tertiary architectural domains of lncRNA RepA

(2017) Fei Liu et al.   Nature Chemical Biology

Biomolecular condensates: organizers of cellular biochemistry

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

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

(2017) Laura E. Ritchey et al.   NUCLEIC ACIDS RESEARCH

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

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

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

(2016) Zhipeng Lu et al.   CELL

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

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

Imaging and force probing RNA by atomic force microscopy

(2016) Peter Schön   METHODS

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

(2016) Zhihong Xue 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

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells

(2016) Matthew J. Smola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

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

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

NF90 isoforms, a new family of cellular proteins involved in viral replication?

(2015) Claudia Patiño et al.   BIOCHIMIE

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner

(2015) Tian Chen et al.   CELL RESEARCH

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

(2015) Chen Davidovich et al.   MOLECULAR CELL

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus

(2015) Sager J. Gosai 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

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

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

(2015) A. Minajigi et al.   SCIENCE

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

(2014) Thomas R. Cech 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

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

Functional long-range RNA–RNA interactions in positive-strand RNA viruses

(2014) Beth L. Nicholson et al.   NATURE REVIEWS MICROBIOLOGY

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

(2014) J. Talkish et al.   RNA

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

(2014) Ian M Silverman et al.   GENOME BIOLOGY

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   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

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 analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

RNA SHAPE analysis in living cells

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

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

Molecular Mechanisms of Long Noncoding RNAs

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

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

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

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

Repeat expansion disease: progress and puzzles in disease pathogenesis

(2010) Albert R. La Spada et al.   NATURE REVIEWS GENETICS

roX RNAs: Non-coding regulators of the male X chromosome in flies

(2010) Ibrahim Ilik et al.   RNA Biology

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

The maternal-to-zygotic transition: a play in two acts

(2009) W. Tadros et al.   DEVELOPMENT