Thirteen dubious ways to detect conserved structural RNAs
Sign Up to like & getrecommendations! Published in 2022 at "IUBMB Life"
DOI: 10.1002/iub.2694
Abstract: Covariation induced by compensatory base substitutions in RNA alignments is a great way to deduce conserved RNA structure, in principle. In practice, success depends on many factors, importantly the quality and depth of the alignment… read more here.
Keywords: rna structure; covariation; conserved rna; thirteen dubious ... See more keywords
RNA structure, binding, and coordination in Arabidopsis
Sign Up to like & getrecommendations! Published in 2017 at "Wiley Interdisciplinary Reviews: RNA"
DOI: 10.1002/wrna.1426
Abstract: From the moment of transcription, up through degradation, each RNA transcript is bound by an ever‐changing cohort of RNA binding proteins. The binding of these proteins is regulated by both the primary RNA sequence, as… read more here.
Keywords: rna secondary; rna; secondary structure; rna structure ... See more keywords
A hybrid framework based on genetic algorithm and simulated annealing for RNA structure prediction with pseudoknots
Sign Up to like & getrecommendations! Published in 2020 at "Journal of King Saud University - Computer and Information Sciences"
DOI: 10.1016/j.jksuci.2020.03.005
Abstract: Abstract RNA structure prediction with pseudoknots is an NP-complete problem, in which an optimal RNA structure with minimum energy is to be computed. In past decades, several methods have been developed to predict RNA structure… read more here.
Keywords: prediction pseudoknots; genetic algorithm; structure; rna structure ... See more keywords
Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Plant"
DOI: 10.1016/j.molp.2018.01.008
Abstract: RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, we… read more here.
Keywords: rna secondary; rice; secondary structure; conservation ... See more keywords
In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.
Sign Up to like & getrecommendations! Published in 2017 at "Methods"
DOI: 10.1016/j.ymeth.2017.04.009
Abstract: RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent… read more here.
Keywords: structure expression; alternative rna; rna; structure ... See more keywords
Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis.
Sign Up to like & getrecommendations! Published in 2023 at "Accounts of chemical research"
DOI: 10.1021/acs.accounts.2c00782
Abstract: ConspectusRNA molecules convey biological information both in their linear sequence and in their base-paired secondary and tertiary structures. Chemical probing experiments, which involve treating an RNA with a reagent that modifies conformationally dynamic nucleotides, have… read more here.
Keywords: rna structure; chemical probing; rna; single molecule ... See more keywords
RNA structure probing reveals the structural basis of Dicer binding and cleavage
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-23607-w
Abstract: It is known that an RNA’s structure determines its biological function, yet current RNA structure probing methods only capture partial structure information. The ability to measure intact (i.e., full length) RNA structures will facilitate investigations… read more here.
Keywords: cleavage; structure probing; dicer; structure ... See more keywords
SHAPE-guided RNA structure homology search and motif discovery.
Sign Up to like & getrecommendations! Published in 2022 at "Nature communications"
DOI: 10.1038/s41467-022-29398-y
Abstract: The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of… read more here.
Keywords: discovery; rna; shape guided; rna structure ... See more keywords
Computational modeling of RNA 3D structure based on experimental data
Sign Up to like & getrecommendations! Published in 2019 at "Bioscience Reports"
DOI: 10.1042/bsr20180430
Abstract: RNA molecules are master regulators of cells. They are involved in a variety of molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. As in the case… read more here.
Keywords: modeling rna; computational modeling; structure; rna structure ... See more keywords
Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants
Sign Up to like & getrecommendations! Published in 2021 at "Biochemical Society Transactions"
DOI: 10.1042/bst20210318
Abstract: RNA folding is an intrinsic property of RNA that serves a key role in every step of post-transcriptional regulation of gene expression, from RNA maturation to translation in plants. Recent developments of genome-wide RNA structure… read more here.
Keywords: rna structure; rna; post transcriptional; transcriptional regulation ... See more keywords
Machine learning for RNA 2D structure prediction benchmarked on experimental data
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbad153
Abstract: Abstract Since the 1980s, dozens of computational methods have addressed the problem of predicting RNA secondary structure. Among them are those that follow standard optimization approaches and, more recently, machine learning (ML) algorithms. The former… read more here.
Keywords: rna structure; structure; learning rna; machine learning ... See more keywords