In-cell RNA structure probing with SHAPE-MaP

Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins

(2017) Joanna Sztuba-Solinska et al.   NUCLEIC ACIDS RESEARCH

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

(2017) Steven Busan et al.   RNA

Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses

(2016) Anna V. Sherwood et al.   Annual Review of Microbiology

An RNA Element That Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations

(2016) Micki M. Kuhlmann et al.   JOURNAL OF VIROLOGY

Many Activities, One Structure: Functional Plasticity of Ribozyme Folds

(2016) Matthew Lau et al.   MOLECULES

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators

(2016) Melissa K. Takahashi et al.   RNA

Direct identification of base-paired RNA nucleotides by correlated chemical probing

(2016) Andrey Krokhotin et al.   RNA

Comparison of SHAPE reagents for mapping RNA structures inside living cells

(2016) Byron Lee et al.   RNA

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

Nucleic acid-binding specificity of human FUS protein

(2015) Xueyin Wang et al.   NUCLEIC ACIDS RESEARCH

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

(2015) Kyle E. Watters et al.   NUCLEIC ACIDS RESEARCH

In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state

(2015) Jennifer L. McGinnis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the architecture of viral RNA genomes

(2015) Beth L Nicholson et al.   Current Opinion in Virology

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

(2015) Christopher A. Lavender et al.   PLoS Computational Biology

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition

(2015) Yasushi Kondo et al.   eLife

Ribosome RNA Assembly Intermediates Visualized in Living Cells

(2014) Jennifer L. McGinnis et al.   BIOCHEMISTRY

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

(2014) Thomas R. Cech et al.   CELL

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

(2014) David Loughrey et al.   NUCLEIC ACIDS RESEARCH

Single-molecule correlated chemical probing of RNA

(2014) P. J. Homan 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

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

(2013) Jillian Tyrrell et al.   BIOCHEMISTRY

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

(2013) Matthew D. Simon 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

Characterizing TDP-43 interaction with its RNA targets

(2013) Amit Bhardwaj et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7)

(2013) R. Turner et al.   RNA

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

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

Genome Regulation by Long Noncoding RNAs

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

The Mechanisms of RNA SHAPE Chemistry

(2012) Jennifer L. McGinnis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA SHAPE analysis in living cells

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

Exploring RNA Structural Codes with SHAPE Chemistry

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

The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks

(2011) Samuel E. Butcher et al.   ACCOUNTS OF CHEMICAL RESEARCH

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara 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

Functional RNA Elements in the Dengue Virus Genome

(2011) Leopoldo G. Gebhard et al.   Viruses-Basel

TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration

(2010) C. Lagier-Tourenne et al.   HUMAN MOLECULAR GENETICS

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

(2010) Jason G Underwood et al.   NATURE METHODS

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

Strong Correlation between SHAPE Chemistry and the Generalized NMR Order Parameter (S2) in RNA

(2008) Costin M. Gherghe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA