Identification of RNA structures and their roles in RNA functions

X Cao, Y Zhang, Y Ding, Y Wan - Nature Reviews Molecular Cell …, 2024 - nature.com
The development of high-throughput RNA structure profiling methods in the past decade has
greatly facilitated our ability to map and characterize different aspects of RNA structures …

Revealing lncRNA structures and interactions by sequencing-based approaches

X Qian, J Zhao, PY Yeung, QC Zhang… - Trends in biochemical …, 2019 - cell.com
Long noncoding RNAs (lncRNAs) have emerged as significant players in almost every level
of gene function and regulation. Thus, characterizing the structures and interactions of …

Advances in RNA 3D structure modeling using experimental data

B Li, Y Cao, E Westhof, Z Miao - Frontiers in genetics, 2020 - frontiersin.org
RNA is a unique bio-macromolecule that can both record genetic information and perform
biological functions in a variety of molecular processes, including transcription, splicing …

Detecting RNA G-quadruplexes (rG4s) in the transcriptome

CK Kwok, G Marsico… - Cold Spring Harbor …, 2018 - cshperspectives.cshlp.org
SUMMARY RNA G-quadruplex (rG4) secondary structures are proposed to play key roles in
fundamental biological processes that include the modulation of transcriptional, co …

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 …

An antisense noncoding RNA enhances translation via localized structural rearrangements of its cognate mRNA

RS Reis, J Deforges, RR Schmidt… - The Plant …, 2021 - academic.oup.com
A large portion of eukaryotic genes are associated with noncoding, natural antisense
transcripts (NATs). Despite sharing extensive sequence complementarity with their sense …

High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast

E Burlacu, F Lackmann, LC Aguilar, S Belikov… - Nature …, 2017 - nature.com
While the protein composition of various yeast 60S ribosomal subunit assembly
intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) …

Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions

K Choudhary, F Deng, S Aviran - Quantitative Biology, 2017 - Wiley Online Library
Background Structure profiling experiments provide single‐nucleotide information on RNA
structure. Recent advances in chemistry combined with application of high‐throughput …

RNA regulations and functions decoded by transcriptome-wide RNA structure probing

M Piao, L Sun, QC Zhang - Genomics, Proteomics and …, 2017 - academic.oup.com
RNA folds into intricate structures that are crucial for its functions and regulations. To date, a
multitude of approaches for probing structures of the whole transcriptome, ie., RNA …

PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures

M Ledda, S Aviran - Genome biology, 2018 - Springer
Establishing a link between RNA structure and function remains a great challenge in RNA
biology. The emergence of high-throughput structure profiling experiments is revolutionizing …