Carbodiimide reagents for the chemical probing of RNA structure in cells

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

(2018) Anthony M. Mustoe et al.   CELL

Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture

(2018) Yizhu Lin et al.   NUCLEIC ACIDS RESEARCH

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing

(2018) Katherine I. Zhou et al.   RNA Biology

Visualizing the secondary and tertiary architectural domains of lncRNA RepA

(2017) Fei Liu et al.   Nature Chemical Biology

The crystal structure of the 5′ functional domain of the transcription riboregulator 7SK

(2017) Denise Martinez-Zapien et al.   NUCLEIC ACIDS RESEARCH

Reconstitution of a functional 7SK snRNP

(2017) John E. Brogie et al.   NUCLEIC ACIDS RESEARCH

Glyoxals as in vivo RNA structural probes of guanine base-pairing

(2017) David Mitchell et al.   RNA

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

(2017) Steven Busan et al.   RNA

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

Solution structure of the 5′-terminal hairpin of the 7SK small nuclear RNA

(2016) Sarah Bourbigot et al.   RNA

RNA binding proteins implicated in Xist-mediated chromosome silencing

(2016) Benoit Moindrot et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

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

(2015) Miles Kubota et al.   Nature Chemical Biology

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

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

(2015) Chun Kit Kwok et al.   TRENDS IN BIOCHEMICAL SCIENCES

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation

(2014) Anne-Valerie Gendrel et al.   Annual Review of Cell and Developmental Biology

Ribosome RNA Assembly Intermediates Visualized in Living Cells

(2014) Jennifer L. McGinnis 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

RNA SHAPE analysis in living cells

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

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

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

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

HEXIM1 targets a repeated GAUC motif in the riboregulator of transcription 7SK and promotes base pair rearrangements

(2010) Isabelle Lebars et al.   NUCLEIC ACIDS RESEARCH

Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome

(2010) K. Sarma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

U30 of 7SK RNA Forms a Specific Photo-cross-link with Hexim1 in the Context of Both a Minimal RNA-binding site and a Fully Reconstituted 7SK/Hexim1/P-TEFb Ribonucleoprotein Complex

(2009) François Bélanger et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolution of 7SK RNA and Its Protein Partners in Metazoa

(2009) M. Marz et al.   MOLECULAR BIOLOGY AND EVOLUTION