Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives

Solayman, Md.; Litfin, Thomas; Singh, Jaswinder; Paliwal, Kuldip K.; Zhou, Yaoqi; Zhan, Jian

doi:10.1093/bib/bbac112

Cited by 19 publications

(9 citation statements)

References 96 publications

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“…Recent advances in cryo-EM technology have resulted in structures of large RNA and protein (RNP) complexes like the spliceosome and ribosome [ 18 , 19 ], suggesting that deriving tertiary structural models for stable structures in large pre-processed RNAs may be possible. Secondary and tertiary RNA structural models can be modelled computationally and incorporate experimental chemical probing data [ 20 ]. These calculated structures can be based on combinations of thermodynamic parameters, machine learning and experiments, including highly cited methods like RNAstructure, mFOLD and others [ 21–27 ].…”

Section: Introductionmentioning

confidence: 99%

How does precursor RNA structure influence RNA processing and gene expression?

2023

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RNA is a fundamental biomolecule that has many purposes within cells. Due to its single-stranded and flexible nature, RNA naturally folds into complex and dynamic structures. Recent technological and computational advances have produced an explosion of RNA structural data. Many RNA structures clearly have regulatory and functional properties. Studying the structure of nascent RNAs is particularly challenging due to their low abundance and long length, but their structures are important because they can influence RNA processing. Precursor RNA processing is a nexus of pathways that determines mature isoform composition and that controls gene expression. In this review, we examine what is known about human nascent RNA structure and the influence of RNA structure on processing of precursor RNAs. These known structures provide examples of how other nascent RNAs may be structured and show how novel RNA structures may influence RNA processing including splicing and polyadenylation. RNA structures can be targeted therapeutically to treat disease.

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Section: Introductionmentioning

confidence: 99%

How does precursor RNA structure influence RNA processing and gene expression?

2023

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“…Further, these direct methods cannot be extended to studying RNA structures in vivo . Several methods of indirect chemical probing of RNA structure use chemical reagents to form covalent adducts or cause cleavage of RNA in regions that are flexible and solvent‐accessible (Solayman et al., 2022; Ziehler & Engelke, 2000). The treated RNA is then used as a substrate for primer extension and reverse transcription (RT), where the RT enzyme mediates RNA‐dependent DNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

Using 5′ ³²P‐labeled Primer and Reverse Transcription to Probe RNA Structure

2023

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RNA molecules perform numerous cellular functions necessary for cell viability, some of which can depend on the RNA's structure. Therefore, it is important to study RNA structure and RNA folding to better understand the molecular basis of these functions. RNA chemical mapping strategies to elucidate RNA structural changes involve using chemical reagents that form adducts or cleave RNA. Selective 2′‐hydroxyl acylation analyzed by primer extension (SHAPE) measures RNA flexibility by modification of the 2′ hydroxyl groups of flexible nucleotides. These RNA adducts can be detected using 32P‐labeled primers and reverse transcription (RT) followed by PAGE analysis. This strategy can reveal the base‐paired regions of the RNA and provide insight into tertiary structure and solvent accessibility. This protocol provides a method to interrogate RNA structure using furoyl acylimidazole (FAI). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Reverse transcription (RT) primer labeling with 32P radionuclide Basic Protocol 2: Characterization of RNA structure with radiolabeled primer and reverse transcription (RT)

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“…To probe the structural properties of RNA, several strategies to detect solvent‐accessible and flexible regions of RNA have been developed (Solayman et al., 2022). These strategies involve either chemical conjugation with a non‐selective reactive species or chemical cleavage of RNA in flexible regions.…”

Section: Introductionmentioning

confidence: 99%

Overview of Chemical Methods to Probe RNA Structure with Radionucleotides

2023

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Structural features of RNA play an important role in its capability to perform various functions in biological systems. To probe structural features, chemical probes are used to conjugate or cleave RNA at solvent‐accessible sites, differentiating between flexible and constrained regions. These conjugates or cleaved products are then detected using reverse transcription (RT), where enzymatic RNA‐dependent DNA primer extension is abruptly halted at the conjugation site or cleavage site. Here, we provide an overview of methods to probe RNA structure in vitro using radioactively labeled DNA primers, which provide a highly sensitive method to visualize RT stop sites with gel electrophoresis. © 2023 Wiley Periodicals LLC.

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Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives

Cited by 19 publications

References 96 publications

How does precursor RNA structure influence RNA processing and gene expression?

How does precursor RNA structure influence RNA processing and gene expression?

Using 5′ ³²P‐labeled Primer and Reverse Transcription to Probe RNA Structure

Overview of Chemical Methods to Probe RNA Structure with Radionucleotides

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Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives

Cited by 19 publications

References 96 publications

How does precursor RNA structure influence RNA processing and gene expression?

How does precursor RNA structure influence RNA processing and gene expression?

Using 5′ 32P‐labeled Primer and Reverse Transcription to Probe RNA Structure

Overview of Chemical Methods to Probe RNA Structure with Radionucleotides

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Product

Resources

About

Using 5′ ³²P‐labeled Primer and Reverse Transcription to Probe RNA Structure