Discovering common stem-loop motifs in unaligned RNA sequences

Hepatitis D virus (HDV) is classified according to eight genotypes. The various genotypes are included in the HDVdb database, where each HDV sequence is specified by its genotype. In this contribution, a mathematical analysis is performed on RNA sequences in HDVdb. The RNA folding predicted structures of the Genbank HDV genome sequences in HDVdb are classified according to their coarse-grain tree-graph representation. The analysis allows discarding in a simple and efficient way the vast majority of the sequences that exhibit a rod-like structure, which is important for the virus replication, to attempt to discover other biological functions by structure consideration. After the filtering, there remain only a small number of sequences that can be checked for their additional stem-loops besides the main one that is known to be responsible for virus replication. It is found that a few sequences contain an additional stem-loop that is responsible for RNA editing or other possible functions. These few sequences are grouped into two main classes, one that is well-known experimentally belonging to genotype 3 for patients from South America associated with RNA editing, and the other that is not known at present belonging to genotype 7 for patients from Cameroon. The possibility that another function besides virus replication reminiscent of the editing mechanism in HDV genotype 3 exists in HDV genotype 7 has not been explored before and is predicted by eigenvalue analysis. Finally, when comparing native and shuffled sequences, it is shown that HDV sequences belonging to all genotypes are accentuated in their mutational robustness and thermodynamic stability as compared to other viruses that were subjected to such an analysis.

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Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress

BioMed Research International ◽

10.1155/2016/7562085 ◽

2016 ◽

Vol 2016 ◽

pp. 1-14 ◽

Cited By ~ 17

Author(s):

Masaru Yoshikawa ◽

Yoichi Robertus Fujii

Keyword(s):

Gene Expression ◽

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Quantum Dynamic ◽

Rna Sequences ◽

Stem Loop ◽

Important Regulator ◽

Multiple Levels ◽

Cellular Stresses ◽

Nucleolar Rnas

Dysfunction of ribosome biogenesis induces divergent ribosome-related diseases including ribosomopathy and occasionally results in carcinogenesis. Although many defects in ribosome-related genes have been investigated, little is known about contribution of ribosomal RNA (rRNA) in ribosome-related disorders. Meanwhile, microRNA (miRNA), an important regulator of gene expression, is derived from both coding and noncoding region of the genome and is implicated in various diseases. Therefore, we performedin silicoanalyses using M-fold, TargetScan, GeneCoDia3, and so forth to investigate RNA relationships between rRNA and miRNA against cellular stresses. We have previously shown that miRNA synergism is significantly correlated with disease and the miRNA package is implicated in memory for diseases; therefore, quantum Dynamic Nexus Score (DNS) was also calculated using MESer program. As a result, seventeen RNA sequences identical with known miRNAs were detected in the human rRNA and termed as rRNA-hosted miRNA analogs (rmiRNAs). Eleven of them were predicted to form stem-loop structures as pre-miRNAs, and especially one stem-loop was completely identical withhsa-pre-miR-3678located in the non-rDNA region. Thus, these rmiRNAs showed significantly high DNS values, participation in regulation of cancer-related pathways, and interaction with nucleolar RNAs, suggesting that rmiRNAs may be stress-responsible resident miRNAs which transmit stress-tuning information in multiple levels.

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Identification of a cis-Acting Replication Element within the Poliovirus Coding Region

Journal of Virology ◽

10.1128/jvi.74.10.4590-4600.2000 ◽

2000 ◽

Vol 74 (10) ◽

pp. 4590-4600 ◽

Cited By ~ 173

Author(s):

Ian Goodfellow ◽

Yasmin Chaudhry ◽

Andrew Richardson ◽

Janet Meredith ◽

Jeffrey W. Almond ◽

...

Keyword(s):

Rna Virus ◽

Site Directed Mutagenesis ◽

Evolutionary Significance ◽

Rna Structures ◽

Coding Region ◽

Rna Sequences ◽

Stem Loop ◽

Cis Acting ◽

Function Recovery ◽

Positive Sense

ABSTRACT The replication of poliovirus, a positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded template. RNA sequences involved in the latter process are poorly defined. Since many sequences involved in picornavirus replication form RNA structures, we searched the genome, other than the untranslated regions, for predicted local secondary structural elements and identified a 61-nucleotide (nt) stem-loop in the region encoding the 2C protein. Covariance analysis suggested the structure was well conserved in the Enterovirus genus of the Picornaviridae. Site-directed mutagenesis, disrupting the structure without affecting the 2C product, destroyed genome viability and suggested that the structure was required in the positive sense for function. Recovery of revertant viruses suggested that integrity of the structure was critical for function, and analysis of replication demonstrated that nonviable mutants did not synthesize negative strands. Our conclusion, that this RNA secondary structure constitutes a novel polioviruscis-acting replication element (CRE), is supported by the demonstration that subgenomic replicons bearing lethal mutations in the native structure can be restored to replication competence by the addition of a second copy of the 61-nt wild-type sequence at another location within the genome. This poliovirus CRE functionally resembles an element identified in rhinovirus type 14 (K. L. McKnight and S. M. Lemon, RNA 4:1569–1584, 1998) and the cardioviruses (P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560–11565, 1999) but differs in sequence, structure, and location. The functional role and evolutionary significance of CREs in the replication of positive-sense RNA viruses is discussed.

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A Review on Recent Computational Methods for Predicting Noncoding RNAs

BioMed Research International ◽

10.1155/2017/9139504 ◽

2017 ◽

Vol 2017 ◽

pp. 1-14 ◽

Cited By ~ 5

Author(s):

Yi Zhang ◽

Haiyun Huang ◽

Dahan Zhang ◽

Jing Qiu ◽

Jiasheng Yang ◽

...

Keyword(s):

Computational Methods ◽

De Novo ◽

Noncoding Rnas ◽

Minimum Free Energy ◽

Rna Sequences ◽

Stem Loop ◽

Third Generation Sequencing ◽

High Efficient ◽

Mapping Technology ◽

Sequencing Platforms

Noncoding RNAs (ncRNAs) play important roles in various cellular activities and diseases. In this paper, we presented a comprehensive review on computational methods for ncRNA prediction, which are generally grouped into four categories: (1) homology-based methods, that is, comparative methods involving evolutionarily conserved RNA sequences and structures, (2) de novo methods using RNA sequence and structure features, (3) transcriptional sequencing and assembling based methods, that is, methods designed for single and pair-ended reads generated from next-generation RNA sequencing, and (4) RNA family specific methods, for example, methods specific for microRNAs and long noncoding RNAs. In the end, we summarized the advantages and limitations of these methods and pointed out a few possible future directions for ncRNA prediction. In conclusion, many computational methods have been demonstrated to be effective in predicting ncRNAs for further experimental validation. They are critical in reducing the huge number of potential ncRNAs and pointing the community to high confidence candidates. In the future, high efficient mapping technology and more intrinsic sequence features (e.g., motif and k-mer frequencies) and structure features (e.g., minimum free energy, conserved stem-loop, or graph structures) are suggested to be combined with the next- and third-generation sequencing platforms to improve ncRNA prediction.

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Characterization of UVA-Induced Alterations to Transfer RNA Sequences

Biomolecules ◽

10.3390/biom10111527 ◽

2020 ◽

Vol 10 (11) ◽

pp. 1527

Author(s):

Congliang Sun ◽

Patrick A. Limbach ◽

Balasubrahmanyam Addepalli

Keyword(s):

Transfer Rna ◽

Rna Modification ◽

Specific Information ◽

Rna Sequences ◽

Stem Loop ◽

Loop Region ◽

Photooxidative Damage ◽

Liquid Chromatography Tandem Mass ◽

Loop Regions

Ultraviolet radiation (UVR) adversely affects the integrity of DNA, RNA, and their nucleoside modifications. By employing liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based RNA modification mapping approaches, we identified the transfer RNA (tRNA) regions most vulnerable to photooxidation. Photooxidative damage to the anticodon and variable loop regions was consistently observed in both modified and unmodified sequences of tRNA upon UVA (λ 370 nm) exposure. The extent of oxidative damage measured in terms of oxidized guanosine, however, was higher in unmodified RNA compared to its modified version, suggesting an auxiliary role for nucleoside modifications. The type of oxidation product formed in the anticodon stem–loop region varied with the modification type, status, and whether the tRNA was inside or outside the cell during exposure. Oligonucleotide-based characterization of tRNA following UVA exposure also revealed the presence of novel photoproducts and stable intermediates not observed by nucleoside analysis alone. This approach provides sequence-specific information revealing potential hotspots for UVA-induced damage in tRNAs.

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An intranasal ASO therapeutic targeting SARS-CoV-2

10.1101/2021.05.17.444397 ◽

2021 ◽

Author(s):

Chi Zhu ◽

Justin Y. Lee ◽

Jia Z. Woo ◽

Lei Xu ◽

Xammy Nguyenla ◽

...

Keyword(s):

Viral Replication ◽

Locked Nucleic Acid ◽

Rna Sequences ◽

Stem Loop ◽

Stem Loop Structure ◽

Promising Therapeutic Approach ◽

Vaccine Distribution ◽

Rapid Deployment

The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identified an LNA ASO binding to the 5′ leader sequence of SARS-CoV-2 ORF1a/b that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the K18-hACE2 humanized COVID-19 mouse model potently (98-99%) suppressed viral replication in the lungs of infected mice, revealing strong prophylactic and treatment effects. We found that the LNA ASO also represses viral infection in golden Syrian hamsters, and is highly efficacious in countering all SARS-CoV-2 "variants of concern" tested in vitro and in vivo, including B.1.427, B.1.1.7, and B.1.351 variants. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce transmission of variants partially resistant to vaccines and monoclonal antibodies, and could be deployed intranasally for prophylaxis or via lung delivery by nebulizer to decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences, and they may have particular impact in areas where vaccine distribution is a challenge, and could be stockpiled for future coronavirus pandemics.

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RNA-Based Regulation of Transcription and Translation of Aureusvirus Subgenomic mRNA1

Journal of Virology ◽

10.1128/jvi.00376-09 ◽

2009 ◽

Vol 83 (19) ◽

pp. 10096-10105 ◽

Cited By ~ 12

Author(s):

Wei Xu ◽

K. Andrew White

Keyword(s):

Coat Protein ◽

Mutational Analysis ◽

Regulation Of Transcription ◽

Rna Structures ◽

Rna Sequences ◽

Stem Loop ◽

Translational Enhancer ◽

Stem Loop Structure ◽

Regulatory Strategies ◽

Rna Interaction

ABSTRACT Cucumber leaf spot virus (CLSV) is an aureusvirus (family Tombusviridae) that has a positive-sense RNA genome encoding five proteins. During infections, CLSV transcribes two subgenomic (sg) mRNAs and the larger of the two, sg mRNA1, encodes coat protein. Here, the viral RNA sequences and structures that regulate transcription and translation of CLSV sg mRNA1 were investigated. A medium-range RNA-RNA interaction in the CLSV genome, spanning 148 nucleotides, was found to be required for the efficient transcription of sg mRNA1. Further analysis indicated that the structure formed by this interaction acted as an attenuation signal required for transcription of sg mRNA1 via a premature termination mechanism. Translation of coat protein from sg mRNA1 was determined to be facilitated by a 5′-terminal stem-loop structure in the message that resembled a tRNA anticodon stem-loop. The results from mutational analysis indicated that the 5′-terminal stem-loop mediated efficient base pairing with a 3′-cap-independent translational enhancer at the 3′ end of the message, leading to efficient translation of coat protein from sg mRNA1. Comparison of the regulatory RNA structures for sg mRNA1 of CLSV to those used by the closely related tombusviruses and certain cellular RNAs revealed interesting differences and similarities that provide evolutionary and mechanistic insights into RNA-based regulatory strategies.

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cis-Acting Sequences of Bacillus subtilis pyrG mRNA Essential for Regulation by Antitermination

Journal of Bacteriology ◽

10.1128/jb.184.23.6734-6738.2002 ◽

2002 ◽

Vol 184 (23) ◽

pp. 6734-6738 ◽

Cited By ~ 8

Author(s):

Qi Meng ◽

Robert L. Switzer

Keyword(s):

Bacillus Subtilis ◽

Regulatory Protein ◽

Leader Region ◽

Ctp Synthetase ◽

Rna Sequences ◽

Stem Loop ◽

Transcription Terminator ◽

Cis Acting ◽

Sequence Deletion ◽

Transcriptional Fusions

ABSTRACT Expression of the Bacillus subtilis pyrG gene, which encodes CTP synthetase, is repressed by cytidine nucleotides. Regulation involves a termination-antitermination mechanism acting at a transcription terminator located within the 5′ untranslated pyrG leader sequence. Deletion and substitution mutagenesis of a series of pyrG′-lacZ transcriptional fusions integrated into the B. subtilis chromosome demonstrated that only the terminator stem-loop and two specific 4- to 6-nucleotide RNA sequences were required for derepression of pyrG by starvation for cytidine nucleotides. The first sequence, GGGC/U, comprises the first four nucleotides at the 5′ end of the pyrG transcript, and the second, GCUCCC, forms the first six nucleotides of the 5′ strand of the terminator stem. All of the nucleotides lying between the two required RNA sequences can be deleted without loss of regulation. We propose that an as-yet-unidentified regulatory protein binds to these two RNA segments and prevents termination of transcription in the pyrG leader region when intracellular CTP levels are low.

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An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Scientifica ◽

10.6064/2012/928783 ◽

2012 ◽

Vol 2012 ◽

pp. 1-17 ◽

Cited By ~ 37

Author(s):

Dmitry M. Kolpashchikov

Keyword(s):

Molecular Beacon ◽

Signal To Noise Ratio ◽

Probe Design ◽

Rna Sequences ◽

Molecular Sensing ◽

Stem Loop ◽

Nucleic Acid Analysis ◽

Loop Shape ◽

Folded Rna ◽

Rna And Dna

Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.

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In silico identification of conserved cis-acting RNA elements in the SARS-CoV-2 genome

Future Virology ◽

10.2217/fvl-2020-0163 ◽

2020 ◽

Vol 15 (7) ◽

pp. 409-417 ◽

Cited By ~ 4

Author(s):

Bader Y Alhatlani

Keyword(s):

Rna Secondary Structure ◽

Rna Sequences ◽

Stem Loop ◽

Cis Acting ◽

Secondary Structure Predictions ◽

Genomic Packaging ◽

Potential Vaccine ◽

In Silico Identification ◽

Rna Elements ◽

Viral Sequences

Aim: The aim of this study was to computationally predict conserved RNA sequences and structures known as cis-acting RNA elements (CREs) in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Materials & methods: Bioinformatics tools were used to analyze and predict CREs by obtaining viral sequences from available databases. Results: Computational analysis revealed the presence of RNA stem-loop structures within the 3′ end of the ORF1ab region analogous to previously identified SARS-CoV genomic packaging signals. Alignment-based RNA secondary structure predictions of the 5′ end of the SARS-CoV-2 genome also identified conserved CREs. Conclusion: These CREs may be potential vaccine and/or antiviral therapeutic targets; however, further studies are warranted to confirm their roles in the SARS-CoV-2 life cycle.

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