Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data

Aviran, Sharon; Incarnato, Danny

doi:10.1016/j.jmb.2022.167635

Cited by 22 publications

(11 citation statements)

References 119 publications

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“…These nucleotides can be specified in a constraint data file. Generally, however, this feature has been superseded by quantification of the extent of accessibility by SHAPE or DMS, which provide more information than binary accessibility (Aviran & Incarnato, 2022; Eddy, 2014; Sloma & Mathews, 2015). Quantified DMS accessibility can be used on the command line of the Fold program by using the ‐‐DMS option (Cordero et al., 2012).…”

Section: Guidelines For Understanding Resultsmentioning

confidence: 99%

RNA Secondary Structure Analysis Using RNAstructure

2023

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RNAstructure is a user‐friendly program for the prediction and analysis of RNA secondary structure. It is available as a web server, a program with a graphical user interface, or a set of command line tools. The programs are available for Microsoft Windows, macOS, or Linux. This article provides protocols for prediction of RNA secondary structure (using the web server, the graphical user interface, or the command line) and high‐affinity oligonucleotide binding sites to a structured RNA target (using the graphical user interface). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Predicting RNA secondary structure using the RNAstructure web server Alternate Protocol 1: Predicting secondary structure and base pair probabilities using the RNAstructure graphical user interface Alternate Protocol 2: Predicting secondary structure and base pair probabilities using the RNAstructure command line interface Basic Protocol 2: Predicting binding affinities of oligonucleotides complementary to an RNA target using OligoWalk

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Section: Guidelines For Understanding Resultsmentioning

confidence: 99%

RNA Secondary Structure Analysis Using RNAstructure

2023

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“…NMR or low‐resolution approaches (e. g., smFRET) often require a time‐consuming effort. Recent computational developments allow for the generation of ensembles from secondary structure probing, which requires deconvolution of the averaged probing data [98] …”

Section: Applications Of Saxs In Rna Biologymentioning

confidence: 99%

“…Recent computational developments allow for the generation of ensembles from secondary structure probing, which requires deconvolution of the averaged probing data. [98] The full conformational space of RNAs is best depicted by SAXS experimentally. Several thousand structures are generated by MD to cover the conformational space as comprehensively as possible.…”

Section: Saxs For the Treatment Of Rna Ensemblesmentioning

confidence: 99%

Advances, Applications, and Perspectives in Small‐Angle X‐ray Scattering of RNA

Tants

Schlundt

2023

ChemBioChem

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RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA‐regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X‐ray crystallography, and cryo‐electron microscopy can provide high‐resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small‐angle X‐ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large‐sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.

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“…Figure 2 is adapted from ref. 68 , CC BY 4.0 (https:// creativecommons.org/licenses/by/4.0/). interactome in vivo 40 (MARIO) and cross-linking of matched RNAs and deep sequencing 41 (COMRADES) were all developed at similar times to capture cross-linked RNA species for transcriptome-scale analyses.…”

Section: Mapping Rna-rna Base-pairing and Through-space Interactionsmentioning

confidence: 99%

“…There are two classes of computational methods available for ensemble deconvolution from bulk structure probing data, which have been recently extensively reviewed elsewhere 68 and will be only briefly discussed here. The first class of methods heavily relies on thermodynamics because they attempt to predict a parsimonious set of structures for a given RNA that can justify the experimental data (Fig.…”

Section: Computational Approaches For Deconvolving Rna Structure Ense...mentioning

confidence: 99%

Probing the dynamic RNA structurome and its functions

2022

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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-throughput sequencing-based RNA structure mapping methods has enabled the rapid in vivo structural interrogation of entire cellular transcriptomes. Collectively, these studies are shedding new light on the long underestimated complexity of the structural organization of the transcriptome -the RNA structurome. Moreover, recent analyses are challenging the view that the RNA structurome is a static entity by revealing how RNA molecules establish intricate networks of alternative intramolecular and intermolecular interactions and that these ensembles of RNA structures are dynamically regulated to finely tune RNA functions in living cells. This new understanding of how RNA can shape cell phenotypes has important implications for the development of RNA-targeted therapeutic strategies.Sections glyoxal and other α-ketoaldehydes, which react with unpaired guanines 14 , and carbodiimide reagents such as 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), which display selectivity for unpaired guanines and uracils, or for G:U wobble pairs 15,16 .By contrast, chemical probing by selective 2′-hydroxyl acylation analysed by primer extension (SHAPE) measures the flexibility of the RNA backbone 17 , which is generally used as a proxy for base-pairing: when the SHAPE reagent forms an adduct with the 2′-OH of a structurally flexible nucleotide, the position is assumed to be unpaired. Moreover, specific structural states have been shown to promote SHAPE Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author selfarchiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

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Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data

Cited by 22 publications

References 119 publications

RNA Secondary Structure Analysis Using RNAstructure

RNA Secondary Structure Analysis Using RNAstructure

Advances, Applications, and Perspectives in Small‐Angle X‐ray Scattering of RNA

Probing the dynamic RNA structurome and its functions

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