4.8 Review

Progress and challenges for chemical probing of RNA structure inside living cells

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo

Yin Tang et al.

BIOINFORMATICS (2015)

Article Multidisciplinary Sciences

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

Colleen A. McHugh et al.

NATURE (2015)

Article Multidisciplinary Sciences

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

Yoichiro Sugimoto et al.

NATURE (2015)

Article Multidisciplinary Sciences

Structural imprints in vivo decode RNA regulatory mechanisms

Robert C. Spitale et al.

NATURE (2015)

Article Biochemical Research Methods

Identification of active transcriptional regulatory elements from GRO-seq data

Charles G. Danko et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark

Meredith Corley et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

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

Jennifer L. McGinnis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Review Biochemistry & Molecular Biology

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

Chun Kit Kwok et al.

TRENDS IN BIOCHEMICAL SCIENCES (2015)

Article Biochemistry & Molecular Biology

Ribosome RNA Assembly Intermediates Visualized in Living Cells

Jennifer L. McGinnis et al.

BIOCHEMISTRY (2014)

Review Biochemistry & Molecular Biology

Towards Understanding RNA-Mediated Neurological Disorders

Ranhui Duan et al.

JOURNAL OF GENETICS AND GENOMICS (2014)

Article Multidisciplinary Sciences

Protein-guided RNA dynamics during early ribosome assembly

Hajin Kim et al.

NATURE (2014)

Review Genetics & Heredity

Insights into RNA structure and function from genome-wide studies

Stefanie A. Mortimer et al.

NATURE REVIEWS GENETICS (2014)

Article Biochemistry & Molecular Biology

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

Ralph D. Hector et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Chemical probing of RNA with the hydroxyl radical at single-atom resolution

Shakti Ingle et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Structural determinants for ligand capture by a class II preQ1 riboswitch

Mijeong Kang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

Jillian Tyrrell et al.

BIOCHEMISTRY (2013)

Review Biochemistry & Molecular Biology

A Decade of Riboswitches

Alexander Serganov et al.

Article Biochemistry & Molecular Biology

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

Zhengqing Ouyang et al.

GENOME RESEARCH (2013)

Article Biochemistry & Molecular Biology

In Vivo X-Ray Footprinting of Pre-30S Ribosomes Reveals Chaperone-Dependent Remodeling of Late Assembly Intermediates

Sarah F. Clatterbuck Soper et al.

MOLECULAR CELL (2013)

Article Multidisciplinary Sciences

The architecture of Tetrahymena telomerase holoenzyme

Jiansen Jiang et al.

NATURE (2013)

Article Biochemistry & Molecular Biology

RNA SHAPE analysis in living cells

Robert C. Spitale et al.

NATURE CHEMICAL BIOLOGY (2013)

Article Biochemical Research Methods

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

Yue Wan et al.

NATURE PROTOCOLS (2013)

Article Biochemistry & Molecular Biology

Conserved arginines on the rim of Hfq catalyze base pair formation and exchange

Subrata Panja et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Determination of in vivo RNA structure in low-abundance transcripts

Chun Kit Kwok et al.

NATURE COMMUNICATIONS (2013)

Article Biochemical Research Methods

Single-molecule mechanical identification and sequencing

Fangyuan Ding et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Hi-C: A comprehensive technique to capture the conformation of genomes

Jon-Matthew Belton et al.

METHODS (2012)

Article Multidisciplinary Sciences

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

George A. Perdrizet et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Kinetic analysis of pre-ribosome structure in vivo

Agata Swiatkowska et al.

Article Biochemistry & Molecular Biology

Association of Argonaute proteins and microRNAs can occur after cell lysis

Kasandra J. Riley et al.

Article Multidisciplinary Sciences

Direct Observation of Cotranscriptional Folding in an Adenine Riboswitch

Kirsten L. Frieda et al.

SCIENCE (2012)

Review Cell Biology

Computational analysis of noncoding RNAs

Stefan Washietl et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2012)

Article Multidisciplinary Sciences

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

Grzegorz Kudla et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

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

Julius B. Lucks et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Review Biochemistry & Molecular Biology

Advances in RNA structure analysis by chemical probing

Kevin M. Weeks

CURRENT OPINION IN STRUCTURAL BIOLOGY (2010)

Review Biochemical Research Methods

SHAPE-directed RNA secondary structure prediction

Justin T. Low et al.

METHODS (2010)

Article Biochemistry & Molecular Biology

RNA folding in living cells

Georgeta Zemora et al.

RNA BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Computational approaches for RNA energy parameter estimation

Mirela Andronescu et al.

Article Biochemistry & Molecular Biology

mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo

Elisabeth M. Mahen et al.

PLOS BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Quantitative Analysis of RNA Solvent Accessibility by N-Silylation of Guanosine

Stefanie A. Mortimer et al.

BIOCHEMISTRY (2009)

Article Multidisciplinary Sciences

Architecture and secondary structure of an entire HIV-1 RNA genome

Joseph M. Watts et al.

NATURE (2009)

Article Multidisciplinary Sciences

Accurate SHAPE-directed RNA structure determination

Katherine E. Deigan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Diversity and Complexity in DNA Recognition by Transcription Factors

Gwenael Badis et al.

SCIENCE (2009)

Article Biochemistry & Molecular Biology

The Vienna RNA Websuite

Andreas R. Gruber et al.

NUCLEIC ACIDS RESEARCH (2008)

Review Cell Biology

RNA-binding proteins: modular design for efficient function

Bradley M. Lunde et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)

Review Biochemical Research Methods

DMS footprinting of structured RNAs and RNA-protein complexes

Pilar Tijerina et al.

NATURE PROTOCOLS (2007)

Article Biochemistry & Molecular Biology

Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast

EM Mahen et al.

MOLECULAR CELL (2005)

Article Chemistry, Multidisciplinary

RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNAAsp transcripts

KA Wilkinson et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Multidisciplinary

RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)

EJ Merino et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Review Biochemistry & Molecular Biology

RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle

R Stefl et al.

EMBO REPORTS (2005)

Article Multidisciplinary Sciences

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

DH Mathews et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

RNA structure of trinucleotide repeats associated with human neurological diseases

K Sobczak et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Effect of transcription on folding of the Tetrahymena ribozyme

SL Heilman-Miller et al.

Article Biochemistry & Molecular Biology

Monitoring intermediate folding states of the td group I intron in vivo

C Waldsich et al.

EMBO JOURNAL (2002)

Article Cell Biology

ASH1 mRNA localization in three acts

DL Beach et al.

MOLECULAR BIOLOGY OF THE CELL (2001)

Article Multidisciplinary Sciences

The structural basis of ribosome activity in peptide bond synthesis

P Nissen et al.

SCIENCE (2000)