RNA Secondary Structure Analysis Using RNAstructure

Mathews, David H.

doi:10.1002/0471250953.bi1206s13

Cited by 96 publications

(99 citation statements)

References 42 publications

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“…Based on the whole genome sequence of HSV-1 (F strain) provided in GenBank (NC_001806), the defined nonencoding region and intron area were scanned using RNA structure 3.2 [19] to predict the secondary structures of the miRNA precursors encoded by the above genes. The candidate hairpin structures that were 70-120 nt in length and had <-20 kcal mol -1 minimum free energy (MFE) were selected for sequence comparison with all the known miRNA sequences in the miRBase database [20,21].…”

Section: Structure Analysis and Prediction Of Mirnamentioning

confidence: 99%

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A microRNA encoded by HSV-1 inhibits a cellular transcriptional repressor of viral immediate early and early genes

Guo²,

Zhang

et al. 2013

Sci. China Life Sci.

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Viral microRNAs are one component of the RNA interference phenomenon generated during viral infection. They were first identified in the Herpesviridae family, where they were found to regulate viral mRNA translation. In addition, prior work has suggested that Kaposi's sarcoma-associated herpesvirus (KSHV) is capable of regulating cellular gene transcription by miRNA. We demonstrate that a miRNA, hsv1-mir-H27, encoded within the genome of herpes simplex virus 1 (HSV-1), targets the mRNA of the cellular transcriptional repressor Kelch-like 24 (KLHL24) that inhibits transcriptional efficiency of viral immediate-early and early genes. The viral miRNA is able to block the expression of KLHL24 in cells infected by HSV-1. Our discovery reveals an effective viral strategy for evading host cell defenses and supporting the efficient replication and proliferation of HSV-1.

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Section: Structure Analysis and Prediction Of Mirnamentioning

confidence: 99%

“…The putative secondary structure of the non-coding regions of the HSV-1 genome was analyzed by using RNA structure 3.2 software [19]. Various miRNA sequences within the HSV-1 genome were further predicted using the miRBase sequence system [20,21].…”

Section: The Mirna Hsv1-mir-h27 Is Identified By Computational Analysmentioning

confidence: 99%

A microRNA encoded by HSV-1 inhibits a cellular transcriptional repressor of viral immediate early and early genes

Guo²,

Zhang

et al. 2013

Sci. China Life Sci.

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“…In this sense, the original 2D Cartesian representation reported by Nandy for describing DNA sequences [63] and the secondary structure inferred by DNA/RNA folding algorithms (Mfold) [67] were used to derive two types of TIs, for the ITS2 gene class.…”

Section: Discussionmentioning

confidence: 99%

“…Mfold implemented in the RNA structure software [67], for the calculation of the spectral moments as TIs. TI2BioP automatically represents natural biopolymers as 2D graphs and straightforward calculates spectral moments series (TIs) to be used either for statistical classification techniques in building alignment-free models for functional classification or for deriving several alignment-free distance matrices, e.g.…”

Section: Ti2biop Softwarementioning

confidence: 99%

TI2BioP — Topological Indices to BioPolymers. A Graphical– Numerical Approach for Bioinformatics

Agüero-Chapin¹,

Ruiz²,

Pérez-Machado³

et al. 2016

Recent Advances in Biopolymers

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We developed a new graphical-numerical method called TI2BioP (Topological Indices to BioPolymers) to estimate topological indices (TIs) from two-dimensional (2D) graphical approaches for the natural biopolymers DNA, RNA and proteins The methodology mainly turns long biopolymeric sequences into 2D artificial graphs such as Cartesian and four-color maps but also reads other 2D graphs from the thermodynamic folding of DNA/RNA strings inferred from other programs. The topology of such 2D graphs is either encoded by node or adjacency matrixes for the calculation of the spectral moments as TIs. These numerical indices were used to build up alignment-free models to the functional classification of biosequences and to calculate alignment-free distances for phylogenetic purposes. The performance of the method was evaluated in highly diverse gene/protein classes, which represents a challenge for current bioinformatics algorithms. TI2BioP generally outperformed classical bioinformatics algorithms in the functional classification of Bacteriocins, ribonucleases III (RNases III), genomic internal transcribed spacer II (ITS2) and adenylation domains (A-domains) of nonribosomal peptide synthetases (NRPS) allowing the detection of new members in these target gene/protein classes. TI2BioP classification performance was contrasted and supported by predictions with sensitive alignment-based algorithms and experimental outcomes, respectively. The new ITS2 sequence isolated from Petrakia sp. was used in our graphical-numerical approach to estimate alignment-free distances for phylogenetic inferences. Despite TI2BioP having been developed for application in bioinformatics, it can be extended to predict interesting features of other biopolymers than DNA and protein sequences. TI2BioP version 2.0 is freely available from http://ti2biop.sourceforge.net/.

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“…Transcribed RNA was purified by sodium acetate and ethanol precipitation and resuspended in nuclease-free water. RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer, and the secondary structures of RNA molecules were predicted using RNAstructure version 4.6 (42).…”

Section: Methodsmentioning

confidence: 99%

A VapBC Toxin-Antitoxin Module Is a Posttranscriptional Regulator of Metabolic Flux in Mycobacteria

et al. 2012

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The largest family of toxin-antitoxin (TA) modules are encoded by the vapBC operons, but their roles in bacterial physiology remain enigmatic. Microarray analysis in Mycobacterium smegmatis overexpressing VapC/VapBC revealed a high percentage of downregulated genes with annotated roles in carbon transport and metabolism, suggesting that VapC was targeting specific metabolic mRNA transcripts. To validate this hypothesis, purified VapC was used to identify the RNA cleavage site in vitro . VapC had RNase activity that was sequence specific, cleaving single-stranded RNA substrates at AUAU and AUAA in vitro and in vivo ( viz ., MSMEG_2121 to MSMEG_2124). A bioinformatic analysis of these regions suggested that an RNA hairpin 3′ of the AUA(U/A) motif is also required for efficient cleavage. VapC-mediated regulation in vivo was demonstrated by showing that MSMEG_2124 ( dhaF ) and MSMEG_2121 ( dhaM ) were upregulated in a Δ vapBC mutant growing on glycerol. The Δ vapBC mutant had a specific rate of glycerol consumption that was 2.4-fold higher than that of the wild type during exponential growth. This increased rate of glycerol consumption was not used for generating bacterial biomass, suggesting that metabolism by the Δ vapBC mutant was uncoupled from growth. These data suggest a model in which VapC regulates the rate of glycerol utilization to match the anabolic demands of the cell, allowing for fine-tuning of the catabolic rate at a posttranscriptional level.

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RNA Secondary Structure Analysis Using RNAstructure

Cited by 96 publications

References 42 publications

A microRNA encoded by HSV-1 inhibits a cellular transcriptional repressor of viral immediate early and early genes

A microRNA encoded by HSV-1 inhibits a cellular transcriptional repressor of viral immediate early and early genes

TI2BioP — Topological Indices to BioPolymers. A Graphical– Numerical Approach for Bioinformatics

A VapBC Toxin-Antitoxin Module Is a Posttranscriptional Regulator of Metabolic Flux in Mycobacteria

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