Genome-wide analysis of RNA secondary structure

PC Bevilacqua, LE Ritchey, Z Su… - Annual review of …, 2016 - annualreviews.org
Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary
structures as a result of intramolecular base pairing. In vivo, these RNA structures are not …

Bridging the gap between in vitro and in vivo RNA folding

KA Leamy, SM Assmann, DH Mathews… - Quarterly reviews of …, 2016 - cambridge.org
Deciphering the folding pathways and predicting the structures of complex three-
dimensional biomolecules is central to elucidating biological function. RNA is single …

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

M Kubota, C Tran, RC Spitale - Nature chemical biology, 2015 - nature.com
Proper gene expression is essential for the survival of every cell. Once thought to be a
passive transporter of genetic information, RNA has recently emerged as a key player in …

[HTML][HTML] Predicting RNA secondary structures from sequence and probing data

R Lorenz, MT Wolfinger, A Tanzer, IL Hofacker - Methods, 2016 - Elsevier
RNA secondary structures have proven essential for understanding the regulatory functions
performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success …

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

Y Ding, CK Kwok, Y Tang, PC Bevilacqua… - Nature protocols, 2015 - nature.com
Abstract Structure-seq is a high-throughput and quantitative method that provides genome-
wide information on RNA structure at single-nucleotide resolution. Structure-seq can be …

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

LE Ritchey, Z Su, Y Tang, DC Tack… - Nucleic acids …, 2017 - academic.oup.com
RNA serves many functions in biology such as splicing, temperature sensing, and innate
immunity. These functions are often determined by the structure of RNA. There is thus a …

Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes in Bacillus subtilis

EA Jolley, H Yakhnin, DC Tack, P Babitzke… - RNA, 2023 - rnajournal.cshlp.org
RNA structure regulates bacterial gene expression by several distinct mechanisms via
environmental and cellular stimuli, one of which is temperature. While some genome-wide …

The evolution of RNA structural probing methods: from gels to next‐generation sequencing

E Mailler, JC Paillart, R Marquet… - Wiley …, 2019 - Wiley Online Library
RNA molecules are important players in all domains of life and the study of the relationship
between their multiple flexible states and the associated biological roles has increased in …

Technique development for probing RNA structure in vivo and genome-wide

PC Bevilacqua, SM Assmann - Cold Spring Harbor …, 2018 - cshperspectives.cshlp.org
How organisms perceive and respond to their surroundings is one of the great questions in
biology. It is clear that RNA plays key roles in sensing. Cellular and environmental cues that …

Dawn of the in vivo RNA structurome and interactome

CK Kwok - Biochemical Society Transactions, 2016 - portlandpress.com
RNA is one of the most fascinating biomolecules in living systems given its structural
versatility to fold into elaborate architectures for important biological functions such as gene …