Probing the dynamic RNA structurome and its functions

RC Spitale, D Incarnato - Nature Reviews Genetics, 2023 - nature.com
RNA is a key regulator of almost every cellular process, and the structures adopted by RNA
molecules are thought to be central to their functions. The recent fast-paced evolution of high …

The roles of structural dynamics in the cellular functions of RNAs

LR Ganser, ML Kelly, D Herschlag… - … reviews Molecular cell …, 2019 - nature.com
RNAs fold into 3D structures that range from simple helical elements to complex tertiary
structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory …

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

NA Siegfried, S Busan, GM Rice, JAE Nelson… - Nature …, 2014 - nature.com
Many biological processes are RNA-mediated, but higher-order structures for most RNAs
are unknown, which makes it difficult to understand how RNA structure governs function …

[HTML][HTML] RNA duplex map in living cells reveals higher-order transcriptome structure

Z Lu, QC Zhang, B Lee, RA Flynn, MA Smith… - Cell, 2016 - cell.com
RNA has the intrinsic property to base pair, forming complex structures fundamental to its
diverse functions. Here, we develop PARIS, a method based on reversible psoralen …

Enhancer RNAs and regulated transcriptional programs

MTY Lam, W Li, MG Rosenfeld, CK Glass - Trends in biochemical sciences, 2014 - cell.com
A large portion of the human genome is transcribed into RNAs without known protein-coding
functions, far outnumbering coding transcription units. Extensive studies of long noncoding …

Mechanisms of long non-coding RNAs in mammalian nervous system development, plasticity, disease, and evolution

JA Briggs, EJ Wolvetang, JS Mattick, JL Rinn, G Barry - Neuron, 2015 - cell.com
Only relatively recently has it become clear that mammalian genomes encode tens of
thousands of long non-coding RNAs (lncRNAs). A striking 40% of these are expressed …

The integral role of RNA in stress granule formation and function

D Campos-Melo, ZCE Hawley… - Frontiers in Cell and …, 2021 - frontiersin.org
Stress granules (SGs) are phase-separated, membraneless, cytoplasmic ribonucleoprotein
(RNP) assemblies whose primary function is to promote cell survival by condensing …

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

MJ Smola, GM Rice, S Busan, NA Siegfried… - Nature protocols, 2015 - nature.com
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit
small electrophilic reagents that react with 2′-hydroxyl groups to interrogate RNA structure …

RNA modifications and structures cooperate to guide RNA–protein interactions

CJT Lewis, T Pan, A Kalsotra - Nature reviews Molecular cell biology, 2017 - nature.com
An emerging body of evidence indicates that post-transcriptional gene regulation relies not
only on the sequence of mRNAs but also on their folding into intricate secondary structures …

Techniques for investigating lncRNA transcript functions in neurodevelopment

T Srinivas, E Siqueira, S Guil - Molecular Psychiatry, 2024 - nature.com
Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are
transcribed from a large portion of the mammalian genome. While hypothesized to have a …