scholarly journals LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2

2021 ◽  
Vol 118 (52) ◽  
pp. e2116269118
Author(s):  
Sizhen Li ◽  
He Zhang ◽  
Liang Zhang ◽  
Kaibo Liu ◽  
Boxiang Liu ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Linear Time ◽  
Pcr Primers ◽  
Sequence Length ◽  
Small Interfering Rnas ◽  
General Technique ◽  
Guide Rnas ◽  
Local Structures ◽  
Long Range Interactions ◽  
Full Length Genome

The constant emergence of COVID-19 variants reduces the effectiveness of existing vaccines and test kits. Therefore, it is critical to identify conserved structures in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes as potential targets for variant-proof diagnostics and therapeutics. However, the algorithms to predict these conserved structures, which simultaneously fold and align multiple RNA homologs, scale at best cubically with sequence length and are thus infeasible for coronaviruses, which possess the longest genomes (∼30,000 nt) among RNA viruses. As a result, existing efforts on modeling SARS-CoV-2 structures resort to single-sequence folding as well as local folding methods with short window sizes, which inevitably neglect long-range interactions that are crucial in RNA functions. Here we present LinearTurboFold, an efficient algorithm for folding RNA homologs that scales linearly with sequence length, enabling unprecedented global structural analysis on SARS-CoV-2. Surprisingly, on a group of SARS-CoV-2 and SARS-related genomes, LinearTurboFold’s purely in silico prediction not only is close to experimentally guided models for local structures, but also goes far beyond them by capturing the end-to-end pairs between 5′ and 3′ untranslated regions (UTRs) (∼29,800 nt apart) that match perfectly with a purely experimental work. Furthermore, LinearTurboFold identifies undiscovered conserved structures and conserved accessible regions as potential targets for designing efficient and mutation-insensitive small-molecule drugs, antisense oligonucleotides, small interfering RNAs (siRNAs), CRISPR-Cas13 guide RNAs, and RT-PCR primers. LinearTurboFold is a general technique that can also be applied to other RNA viruses and full-length genome studies and will be a useful tool in fighting the current and future pandemics.

VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment

2021 ◽  
Author(s):  
Rajan Saha Raju ◽  
Abdullah Al Nahid ◽  
Preonath Shuvo ◽  
Rashedul Islam
Keyword(s):  
Genome Sequence ◽  
Rna Viruses ◽  
Hierarchical Classification ◽  
Classification Problem ◽  
Virus Genome ◽  
Taxonomic Classification ◽  
Dna Viruses ◽  
Dna And Rna ◽  
Full Length Genome

AbstractTaxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences.AvailabilityOnline version of VirusTaxo is available at https://omics-lab.com/virustaxo/.

scholarly journals Human Argonaute2 and Argonaute3 are catalytically activated by different lengths of guide RNA

2020 ◽  
Author(s):  
Mi Seul Park ◽  
GeunYoung Sim ◽  
Audrey C. Kehling ◽  
Kotaro Nakanishi
Keyword(s):  
Gene Silencing ◽  
Fold Increase ◽  
Specific Gene ◽  
Small Interfering Rnas ◽  
Guide Rna ◽  
Guide Rnas ◽  
Argonaute Proteins ◽  
Complementary Rnas ◽  
Standing Question

AbstractRNA interfering is a eukaryote-specific gene silencing by 20∼23 nucleotide (nt) microRNAs and small interfering RNAs that recruit Argonaute proteins to complementary RNAs for degradation. In humans, Argonaute2 (AGO2) has been known as the only slicer while Argonaute3 (AGO3) barely cleaves RNAs. Therefore, the intrinsic slicing activity of AGO3 remains controversial and a long-standing question. Here, we report 14-nt 3′ end-shortened variants of let-7a, miR-27a, and specific miR-17-92 families that make AGO3 an extremely competent slicer by an ∼ 82-fold increase in target cleavage. These RNAs, named cleavage-inducing tiny guide RNAs (cityRNAs), conversely lower the activity of AGO2, demonstrating that AGO2 and AGO3 have different optimum guide lengths for target cleavage. Our study sheds light on the role of tiny guide RNAs.

scholarly journals Efficient inhibition of HIV using CRISPR/Cas13d nuclease system

2021 ◽  
Author(s):  
Hoang Nguyen ◽  
Hannah Wilson ◽  
Sahana Jayakumar ◽  
Viraj Kulkarni ◽  
Smita Kulkarni
Keyword(s):  
T Cells ◽  
Alternative Treatment ◽  
Treatment Modality ◽  
Rna Viruses ◽  
Guide Rnas ◽  
Rna Targeting ◽  
Latently Infected ◽  
Infected Cells ◽  
Latent Hiv ◽  
Hiv 1

Recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas13 proteins are programmable RNA-guided ribonucleases that target single-stranded RNA (ssRNA). CRISPR/Cas13 mediated RNA targeting has emerged as a powerful tool for detecting and eliminating RNA viruses. Here, we demonstrate the effectiveness of CRISPR/Cas13d to inhibit HIV-1 replication. We designed guide RNAs (gRNAs) targeting highly conserved regions of HIV-1. RfxCas13d (CasRx) in combination with HIV-specific gRNAs efficiently inhibited HIV-1 replication in cell line models. Furthermore, simultaneous targeting of four distinct sites in the HIV-1 transcript resulted in robust inhibition of HIV-1 replication. We also show the effective HIV-1 inhibition in primary CD4+ T-cells and suppression of HIV-1 reactivated from latently infected cells using the CRISPR/Cas13d system. Our study demonstrates the utility of the CRISPR/Cas13d nuclease system to target acute and latent HIV infection and provides an alternative treatment modality against HIV.

scholarly journals On the verge of life: Distribution of nucleotide sequences in viral RNAs

2021 ◽  
Author(s):  
Mykola Husev ◽  
Andrij Rovenchak
Keyword(s):  
Rna Viruses ◽  
Nucleotide Sequences ◽  
Sequence Length ◽  
Life Distribution ◽  
Frequency Distributions ◽  
Classification Of Diseases ◽  
Negative Hypergeometric Distribution ◽  
Human Coronaviruses ◽  
Best Fit

Abstract The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used to obtain the nucleotide sequences; In the first one, chunks of equal length (four nucleotides) are considered. In the second approach, the whole RNA genome is divided into parts by adenine or the most frequent nucleotide as a "space''. Rank--frequency distributions are studied in both cases. The defined nucleotide sequences are signs comparable to a certain extent to syllables or words as seen from the nature of their rank--frequency distributions. Within the first approach, the P\'olya and the negative hypergeometric distribution yield the best fit. For the distributions obtained within the second approach, we have calculated a set of parameters, including entropy, mean sequence length, and its dispersion. The calculated parameters became the basis for the classification of viruses. We observed that proximity of viruses on planes spanned on various pairs of parameters corresponds to related species. In certain cases, such a proximity is observed for unrelated species as well calling thus for the expansion of the set of parameters used in the classification. We also observed that the fourth most frequent nucleotide sequences obtained within the second approach are of different nature in case of human coronaviruses (different nucleotides for MERS, SARS-CoV, and SARS-CoV-2 versus identical nucleotides for four other coronaviruses). We expect that our findings will be useful as a supplementary tool in the classification of diseases caused by RNA viruses with respect to severity and contagiousness.

scholarly journals LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i258-i267 ◽  
Author(s):  
He Zhang ◽  
Liang Zhang ◽  
David H Mathews ◽  
Liang Huang
Keyword(s):  
Free Energy ◽  
Partition Function ◽  
Structure Prediction ◽  
Linear Time ◽  
Minimum Free Energy ◽  
Supplementary Information ◽  
Sequence Length ◽  
Energy Structure ◽  
Base Pairing ◽  
Long Distance

Abstract Motivation RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy methods to partition function-based methods that account for folding ensembles and can therefore estimate structure and base pair probabilities. However, the classical partition function algorithm scales cubically with sequence length, and is therefore prohibitively slow for long sequences. This slowness is even more severe than cubic-time free energy minimization due to a substantially larger constant factor in runtime. Results Inspired by the success of our recent LinearFold algorithm that predicts the approximate minimum free energy structure in linear time, we design a similar linear-time heuristic algorithm, LinearPartition, to approximate the partition function and base-pairing probabilities, which is shown to be orders of magnitude faster than Vienna RNAfold and CONTRAfold (e.g. 2.5 days versus 1.3 min on a sequence with length 32 753 nt). More interestingly, the resulting base-pairing probabilities are even better correlated with the ground-truth structures. LinearPartition also leads to a small accuracy improvement when used for downstream structure prediction on families with the longest length sequences (16S and 23S rRNAs), as well as a substantial improvement on long-distance base pairs (500+ nt apart). Availability and implementation Code: http://github.com/LinearFold/LinearPartition; Server: http://linearfold.org/partition. Supplementary information Supplementary data are available at Bioinformatics online.

Full‐length genome sequencing of RNA viruses—How the approach can enlighten us on hepatitis C and hepatitis E viruses

2020 ◽  
Author(s):  
Elodie Laugel ◽  
Cédric Hartard ◽  
Hélène Jeulin ◽  
Sibel Berger ◽  
Véronique Venard ◽  
...  
Keyword(s):  
Hepatitis C ◽  
Genome Sequencing ◽  
Rna Viruses ◽  
Hepatitis E ◽  
Full Length ◽  
Full Length Genome

scholarly journals Cas13b-dependent and Cas13b-independent RNA knockdown of viral sequences in mosquito cells following guide RNA expression

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Priscilla Ying Lei Tng ◽  
Leonela Carabajal Paladino ◽  
Sebald Alexander Nkosana Verkuijl ◽  
Jessica Purcell ◽  
Andres Merits ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Strong Suppression ◽  
Rna Molecules ◽  
Guide Rna ◽  
Guide Rnas ◽  
Mosquito Cells ◽  
Independent Effects ◽  
Rna Knockdown ◽  
Viral Sequences ◽  
Potential Use

AbstractAedes aegypti and Aedes albopictus mosquitoes are vectors of the RNA viruses chikungunya (CHIKV) and dengue that currently have no specific therapeutic treatments. The development of new methods to generate virus-refractory mosquitoes would be beneficial. Cas13b is an enzyme that uses RNA guides to target and cleave RNA molecules and has been reported to suppress RNA viruses in mammalian and plant cells. We investigated the potential use of the Prevotella sp. P5-125 Cas13b system to provide viral refractoriness in mosquito cells, using a virus-derived reporter and a CHIKV split replication system. Cas13b in combination with suitable guide RNAs could induce strong suppression of virus-derived reporter RNAs in insect cells. Surprisingly, the RNA guides alone (without Cas13b) also gave substantial suppression. Our study provides support for the potential use of Cas13b in mosquitoes, but also caution in interpreting CRISPR/Cas data as we show that guide RNAs can have Cas-independent effects.

An Insight on RNA Based Therapeutics and Vaccines: Challenges and Opportunities

2021 ◽  
Vol 21 ◽  
Author(s):  
Kanisht Batra ◽  
Sushila Maan ◽  
Anju Sehrawat
Keyword(s):  
Physicochemical Characteristics ◽  
Technological Advancement ◽  
Small Interfering Rnas ◽  
Vaccine Platform ◽  
Promising Alternative ◽  
Rna Molecules ◽  
Guide Rnas ◽  
Drug Molecules ◽  
Challenges And Opportunities

: In this era, RNA molecules have provided a unique opportunity to researchers all over the world for expanding their range of targets in the development of drugs. Due to the unique pharmacological as well as physicochemical characteristics of different RNA molecules such as aptamers, small interfering RNAs (siRNA), antisense oligonucleotides (ASO) and guide RNAs (gRNA), they have emerged recently as a new class of drugs. They are used for selective action on proteins and genes that were not possible to target by conventional drug molecules. These RNA molecules like guide RNAs are also components of novel gene editing mechanisms which can modify the genome nearly in all cells. Vaccines based on RNA molecules have also provided a promising alternative to conventional live attenuated vaccines. RNA based vaccines have high potency, can be rapidly developed, and have potential for manufacturing at a cheaper rate and safe administration. However, the application of these RNAs has been restricted by the high instability and inefficient in vivo delivery. Technological advancement needs to overcome these issues so that RNA based drugs targeting several diseases can be developed. This article emphasizes the potential of RNA based drugs and the major barriers associated with the development of RNA therapeutics. Additionally, the role of RNA based vaccines and their challenges in advancing this promising vaccine platform for the prevention of infectious diseases have been discussed.

scholarly journals Plant Virus-Derived Small Interfering RNAs Originate Predominantly from Highly Structured Single-Stranded Viral RNAs

2005 ◽  
Vol 79 (12) ◽  
pp. 7812-7818 ◽  
Author(s):  
Attila Molnár ◽  
Tibor Csorba ◽  
Lóránt Lakatos ◽  
Éva Várallyay ◽  
Christophe Lacomme ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Small Interfering Rnas ◽  
Double Stranded Rna ◽  
Positive Strand ◽  
Posttranscriptional Gene Silencing ◽  
System A ◽  
Rna Duplexes ◽  
Positive Strand Rna ◽  
Dicer Cleavage ◽  
Pds Gene

ABSTRACT RNA silencing is conserved in a broad range of eukaryotes and includes the phenomena of RNA interference in animals and posttranscriptional gene silencing (PTGS) in plants. In plants, PTGS acts as an antiviral system; a successful virus infection requires suppression or evasion of the induced silencing response. Small interfering RNAs (siRNAs) accumulate in plants infected with positive-strand RNA viruses and provide specificity to this RNA-mediated defense. We present here the results of a survey of virus-specific siRNAs characterized by a sequence analysis of siRNAs from plants infected with Cymbidium ringspot tombusvirus (CymRSV). CymRSV siRNA sequences have a nonrandom distribution along the length of the viral genome, suggesting that there are hot spots for virus-derived siRNA generation. CymRSV siRNAs bound to the CymRSV p19 suppressor protein have the same asymmetry in strand polarity as the sequenced siRNAs and are imperfect double-stranded RNA duplexes. Moreover, an analysis of siRNAs derived from two other nonrelated positive-strand RNA viruses showed that they displayed the same asymmetry as CymRSV siRNAs. Finally, we show that Tobacco mosaic virus (TMV) carrying a short inverted repeat of the phytoene desaturase (PDS) gene triggered more accumulation of PDS siRNAs than the corresponding antisense PDS sequence. Taken together, these results suggest that virus-derived siRNAs originate predominantly by direct DICER cleavage of imperfect duplexes in the most folded regions of the positive strand of the viral RNA.

Sign in / Sign up

Export Citation Format

Share Document