scholarly journals A Comprehensive Analysis of cis-Acting RNA Elements in the SARS-CoV-2 Genome by a Bioinformatics Approach

2020 ◽  
Vol 11 ◽  
Author(s):  
Firoz Ahmed ◽  
Monika Sharma ◽  
Abdulsalam Abdullah Al-Ghamdi ◽  
Sultan Muhammad Al-Yami ◽  
Abdulaziz Musa Al-Salami ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Rna Structure ◽  
Viral Genome ◽  
Genomic Sequence ◽  
Evolutionary Relationship ◽  
Cis Acting ◽  
Full Genomic Sequence ◽  
Rna Elements ◽  
Global Threat ◽  
Genomic Regions

The emergence of a new coronavirus (CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for severe respiratory disease in humans termed coronavirus disease of 2019 (COVID-19), became a new global threat for health and the economy. The SARS-CoV-2 genome is about a 29,800-nucleotide-long plus-strand RNA that can form functionally important secondary and higher-order structures called cis-acting RNA elements. These elements can interact with viral proteins, host proteins, or other RNAs and be involved in regulating translation and replication processes of the viral genome and encapsidation of the virus. However, the cis-acting RNA elements and their biological roles in SARS-CoV-2 as well as their comparative analysis in the closely related viral genome have not been well explored, which is very important to understand the molecular mechanism of viral infection and pathogenies. In this study, we used a bioinformatics approach to identify the cis-acting RNA elements in the SARS-CoV-2 genome. Initially, we aligned the full genomic sequence of six different CoVs, and a phylogenetic analysis was performed to understand their evolutionary relationship. Next, we predicted the cis-acting RNA elements in the SARS-CoV-2 genome using the structRNAfinder tool. Then, we annotated the location of these cis-acting RNA elements in different genomic regions of SARS-CoV-2. After that, we analyzed the sequence conservation patterns of each cis-acting RNA element among the six CoVs. Finally, the presence of cis-acting RNA elements across different CoV genomes and their comparative analysis was performed. Our study identified 12 important cis-acting RNA elements in the SARS-CoV-2 genome; among them, Corona_FSE, Corona_pk3, and s2m are highly conserved across most of the studied CoVs, and Thr_leader, MAT2A_D, and MS2 are uniquely present in SARS-CoV-2. These RNA structure elements can be involved in viral translation, replication, and encapsidation and, therefore, can be potential targets for better treatment of COVID-19. It is imperative to further characterize these cis-acting RNA elements experimentally for a better mechanistic understanding of SARS-CoV-2 infection and therapeutic intervention.

scholarly journals Atypical RNA Elements Modulate Translational Readthrough in Tobacco Necrosis Virus D

2017 ◽  
Vol 91 (8) ◽  
Author(s):  
Laura R. Newburn ◽  
K. Andrew White
Keyword(s):  
Rna Structure ◽  
Viral Genome ◽  
Tobacco Necrosis Virus ◽  
Virus Infectivity ◽  
Necrosis Virus ◽  
Stem Loop ◽  
Content Type ◽  
Translational Readthrough ◽  
Rna Elements ◽  
Positive Strand Rna

ABSTRACT Tobacco necrosis virus, strain D (TNV-D), is a positive-strand RNA virus in the genus Betanecrovirus and family Tombusviridae. The production of its RNA-dependent RNA polymerase, p82, is achieved by translational readthrough. This process is stimulated by an RNA structure that is positioned immediately downstream of the recoding site, termed the readthrough stem-loop (RTSL), and a sequence in the 3′ untranslated region of the TNV-D genome, called the distal readthrough element (DRTE). Notably, a base pairing interaction between the RTSL and the DRTE, spanning ∼3,000 nucleotides, is required for enhancement of readthrough. Here, some of the structural features of the RTSL, as well as RNA sequences and structures that flank either the RTSL or DRTE, were investigated for their involvement in translational readthrough and virus infectivity. The results revealed that (i) the RTSL-DRTE interaction cannot be functionally replaced by stabilizing the RTSL structure, (ii) a novel tertiary RNA structure positioned just 3′ to the RTSL is required for optimal translational readthrough and virus infectivity, and (iii) these same activities also rely on an RNA stem-loop located immediately upstream of the DRTE. Functional counterparts for the RTSL-proximal structure may also be present in other tombusvirids. The identification of additional distinct RNA structures that modulate readthrough suggests that regulation of this process by genomic features may be more complex than previously appreciated. Possible roles for these novel RNA elements are discussed. IMPORTANCE The analysis of factors that affect recoding events in viruses is leading to an ever more complex picture of this important process. In this study, two new atypical RNA elements were shown to contribute to efficient translational readthrough of the TNV-D polymerase and to mediate robust viral genome accumulation in infections. One of the structures, located close to the recoding site, could have functional equivalents in related genera, while the other structure, positioned 3′ proximally in the viral genome, is likely limited to betanecroviruses. Irrespective of their prevalence, the identification of these novel RNA elements adds to the current repertoire of viral genome-based modulators of translational readthrough and provides a notable example of the complexity of regulation of this process.

scholarly journals Functionally interchangeable cis-acting RNA elements in both genome segments of a picorna-like plant virus

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Jiangbo Guo ◽  
Junping Han ◽  
Junyan Lin ◽  
John Finer ◽  
Anne Dorrance ◽  
...  
Keyword(s):  
Plant Virus ◽  
Cis Acting ◽  
Rna Elements

scholarly journals Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

2021 ◽  
Author(s):  
Zhen Tian ◽  
Xiaodong Qin ◽  
Hui Wang ◽  
Ji Li ◽  
Jinfeng Chen
Keyword(s):  
Floral Induction ◽  
Structural Characteristics ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Biological Functions ◽  
Promoter Regions ◽  
Cucumis Sativus L ◽  
Cis Acting ◽  
Genome Wide ◽  
Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

5' and 3' cis-Acting RNA Elements Required for RNA Replication of Porcine Reproductive and Respiratory Syndrome Virus

2007 ◽  
Vol 37 (3) ◽  
pp. 193 ◽  
Author(s):  
Shien-Young Kang ◽  
Yu-Jeong Choi ◽  
Sang-Im Yun ◽  
Byung-Hak Song ◽  
Young-Min Lee
Keyword(s):  
Rna Replication ◽  
Respiratory Syndrome Virus ◽  
Cis Acting ◽  
Rna Elements

scholarly journals dbVar structural variant cluster set for data analysis and variant comparison

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 673 ◽  
Author(s):  
Lon Phan ◽  
Jeffrey Hsu ◽  
Le Quang Minh Tri ◽  
Michaela Willi ◽  
Tamer Mansour ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Chromosomal Rearrangements ◽  
Copy Number Variations ◽  
Structural Variant ◽  
Variant Type ◽  
External Data ◽  
Cluster Set ◽  
Genomic Location ◽  
Complex Chromosomal Rearrangements ◽  
Genomic Regions

dbVar houses over 3 million submitted structural variants (SSV) from 120 human studies including copy number variations (CNV), insertions, deletions, inversions, translocations, and complex chromosomal rearrangements. Users can submit multiple SSVs to dbVAR  that are presumably identical, but were ascertained by different platforms and samples,  to calculate whether the variant is rare or common in the population and allow for cross validation. However, because SSV genomic location reporting can vary – including fuzzy locations where the start and/or end points are not precisely known – analysis, comparison, annotation, and reporting of SSVs across studies can be difficult. This project was initiated by the Structural Variant Comparison Group for the purpose of generating a non-redundant set of genomic regions defined by counts of concordance for all human SSVs placed on RefSeq assembly GRCh38 (RefSeq accession GCF_000001405.26). We intend that the availability of these regions, called structural variant clusters (SVCs), will facilitate the analysis, annotation, and exchange of SV data and allow for simplified display in genomic sequence viewers for improved variant interpretation. Sets of SVCs were generated by variant type for each of the 120 studies as well as for a combined set across all studies. Starting from 3.64 million SSVs, 2.5 million and 3.4 million non-redundant SVCs with count >=1 were generated by variant type for each study and across all studies, respectively. In addition, we have developed utilities for annotating, searching, and filtering SVC data in GVF format for computing summary statistics, exporting data for genomic viewers, and annotating the SVC using external data sources.

scholarly journals RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome

2018 ◽  
Author(s):  
Weizhong Chen ◽  
Zhangming Yan ◽  
Simin Li ◽  
Norman Huang ◽  
Xuerui Huang ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Genomic Sequence ◽  
Single Cells ◽  
Regulation Of Gene Expression ◽  
Nuclear Genome ◽  
Fold Increase ◽  
Nuclear Speckles ◽  
Nuclear Speckle ◽  
Interaction Sites ◽  
Genomic Regions

AbstractNuclear speckles are interchromatin structures enriched in RNA splicing factors. Determining their relative positions with respect to the folded nuclear genome could provide critical information on co-and post-transcriptional regulation of gene expression. However, it remains challenging to identify which parts of the nuclear genome are in proximity to nuclear speckles, due to physical separation between nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNAs, 7SK and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA,nuclearspeckleassociated RNA), may extend to sufficient proximity to the nuclear genome. Leveraging a transcriptome-genome interaction assay (MARGI), we identified nsaRNA-interacting genomic sequences, which exhibited clustering patterns (nsaPeaks) in the genome, suggesting existence of relatively stable interaction sites for nsaRNAs in nuclear genome. Posttranscriptional pre-mRNAs, which are known to be clustered to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Furthermore, CDK9 proteins that localize to the vicinity of nuclear speckles produced ChIP-seq peaks that overlapped with nsaPeaks. Our combined DNA FISH and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs locate in sufficient proximity to nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.

scholarly journals Patterns of Genomic Sequence Diversity among Their Simian Immunodeficiency Viruses Suggest that L'Hoest Monkeys (Cercopithecus lhoesti) Are a Natural Lentivirus Reservoir

2000 ◽  
Vol 74 (8) ◽  
pp. 3892-3898 ◽  
Author(s):  
Brigitte E. Beer ◽  
Elizabeth Bailes ◽  
George Dapolito ◽  
Barbara J. Campbell ◽  
Robert M. Goeken ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Democratic Republic ◽  
Genomic Sequence ◽  
Democratic Republic Of Congo ◽  
Vervet Monkeys ◽  
Genome Sequences ◽  
Distinct Cluster ◽  
Immunodeficiency Virus ◽  
Genomic Regions ◽  
Full Length Genome

ABSTRACT Recently, we described a novel simian immunodeficiency virus (SIVlhoest) from a wild-caught L'Hoest monkey (Cercopithecus lhoesti) from a North American zoo. To investigate whether L'Hoest monkeys are the natural host for these viruses, we have screened blood samples from 14 wild animals from the Democratic Republic of Congo. Eight (57%) were found to be seropositive for SIV. Nearly full-length genome sequences were obtained for SIV isolates from three of these monkeys and compared to the original isolate and to other SIVs. The four samples of SIVlhoest formed a distinct cluster in phylogenetic trees. Two of these isolates differed on average at only about 5% of nucleotides, suggesting that they were epidemiologically linked; otherwise, the SIVlhoest isolates differed on average by 18%. Both the level of diversity and the pattern of its variation along the genome were very similar to those seen among isolates of SIVagm from vervet monkeys, pointing to similarities in the nature of, and constraints on, SIV evolution in these two species. Discordant phylogenetic relationships among the SIVlhoest isolates for different genomic regions indicated that mosaic viruses have been generated by recombination, implying that individual monkeys have been coinfected by more than one strain of SIV. Taken together, these observations provide strong evidence that L'Hoest monkeys constitute a natural reservoir for SIV.

Comparative analysis of two genomic regions among four strains of Buchnera aphidicola, primary endosymbiont of aphids

Gene ◽  
2005 ◽  
Vol 345 (1) ◽  
pp. 73-80 ◽  
Author(s):  
Vicente Pérez-Brocal ◽  
Amparo Latorre ◽  
Rosario Gil ◽  
Andrés Moya
Keyword(s):  
Comparative Analysis ◽  
Buchnera Aphidicola ◽  
Genomic Regions

Chloroplast genomes of seven species of Coryloideae (Betulaceae): structures and comparative analysis

Genome ◽  
2020 ◽  
Vol 63 (7) ◽  
pp. 337-348
Author(s):  
Guanglong Hu ◽  
Lili Cheng ◽  
Wugang Huang ◽  
Qingchang Cao ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Information ◽  
Molecular Breeding ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Mutational Hotspots ◽  
The Family ◽  
Identification Of Species

Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera: Carpinus, Corylus, Ostrya, and Ostryopsis. We sequenced the plastomes of six species of Corylus and one species of Ostryopsis for comparative and phylogenetic analyses. The plastomes are 159–160 kb long and possess typical quadripartite cp architecture. The plastomes show moderate divergence and conserved arrangement. Five mutational hotspots were identified by comparing the plastomes of seven species of Coryloideae: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1. We assembled the most complete phylogenomic tree for the family Betulaceae using 68 plastomes. Our cp genomic sequence phylogenetic analyses placed Carpinus, Ostrya, and Ostryopsis in a clade together and left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the existence of five subclades reflecting the phylogeographical relationships among the species. The data offer significant genetic information for the identification of species of the Coryloideae, taxonomic and phylogenetic studies, and molecular breeding.

Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae

Holzforschung ◽  
2017 ◽  
Vol 71 (3) ◽  
pp. 189-197 ◽  
Author(s):  
Chia-Chen Wu ◽  
Fang-Hua Chu ◽  
Cheng-Kuen Ho ◽  
Chia-Hsuan Sung ◽  
Shu-Hwa Chang
Keyword(s):  
Phylogenetic Analysis ◽  
Liquid Chromatography ◽  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Genomic Sequence ◽  
Ultra Performance Liquid Chromatography ◽  
Chemical Components ◽  
Complete Chloroplast Genome ◽  
Medicinal Fungus ◽  
Indel Markers

Abstract Cinnamomum micranthum (Hayata) Hayata is a tree species that is often confused with Cinnamomum kanehirae Hayata, which is an endemic species in Taiwan and the sole natural host of the valuable medicinal fungus Antrodia cinnamomea. However, the two species are highly similar in morphology and difficult to distinguish based on traditional vegetative structures or wood anatomical methods. The aim of the present study was to identify of these two species by DNA and chemical analysis. The complete chloroplast genome of C. micranthum has been determined and compared with that of C. kanehirae. The leaf methanol extracts of these species were also analyzed by ultra-performance liquid chromatography (UPLC). The length of the C. micranthum chloroplast genome was 152675 bp, i.e. 25 bp shorter than that of C. kanehirae. In phylogenetic analysis, C. micranthum was more closely related to C. kanehirae than other six Lauracea species. Six validated insertion/deletions of bases in the DNA (InDels) are suitable for differentiation of the two species. Moreover, high amounts of linalool and sesamin were present in the leaves of C. kanehirae, but not in C. micranthum. Overall, this study provided new insight for distinguishing the two species on the basis of the chemical composition of the leaves and the InDel markers.

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