2018
DOI: 10.3389/fmicb.2017.02582
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Abstract: Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being us… Show more

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Cited by 28 publications
(18 citation statements)
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References 225 publications
(300 reference statements)
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“…However, we report here that the SARS-CoV-2 genomic RNA is nearly twice as compact and structured as HCV based on its folding stability, even when adjusting for its vastly greater overall length (~ 30 kb vs. ~10 kb). RNA structural motifs within the UTRs and ORFs of coronaviruses are seemingly larger and more complex than those observed in other virus families (Clyde and Harris 2006; Lim and Brown 2017;Li et al 2018;Simon et al 2019), suggesting that an understanding of coronavirus RNA structure will play a key role in understanding the mechanistic processes and vulnerabilities of this virus.…”
Section: Discussionmentioning
confidence: 96%
“…However, we report here that the SARS-CoV-2 genomic RNA is nearly twice as compact and structured as HCV based on its folding stability, even when adjusting for its vastly greater overall length (~ 30 kb vs. ~10 kb). RNA structural motifs within the UTRs and ORFs of coronaviruses are seemingly larger and more complex than those observed in other virus families (Clyde and Harris 2006; Lim and Brown 2017;Li et al 2018;Simon et al 2019), suggesting that an understanding of coronavirus RNA structure will play a key role in understanding the mechanistic processes and vulnerabilities of this virus.…”
Section: Discussionmentioning
confidence: 96%
“…The initial search within a library of viral reference genomes (see Methods) identified two potential sequences among Luteoviridae; Poleroviruses : wheat leaf yellowing-associated virus isolate JN-U3 (GenBank ID # NC_035451; Infernal E-value = 0.00025, score = 44.3) and sugarcane yellow leaf virus (GenBank #NC_000874; Infernal E-value = 6.5, score = 24.2). With these sequences added to the alignment, subsequent searches identified > 40 candidates within the public repository of all available sequences for Tombusviridae and Luteoviridae , demonstrating how powerful this tool is for computationally identifying functional elements in viral RNAs 28 .…”
Section: Resultsmentioning
confidence: 99%
“…Across viral species, CAEs are conserved at the 5' and 3' ends, forming secondary structures such as stem loops and higher order structures that aid genomic stability or increase interaction with TAEs (5). Function can be often inferred from location, with 5' CAEs correlating to replication and initiation of translation, and 3' CAEs to nuclear export, RNA processing and RNA stability (6). CAEs can also be found within gene-coding regions and function in ribosomal frameshifting, RNA replication, and specifying the RNA for encapsidation (5).…”
Section: Introductionmentioning
confidence: 99%
“…TIPs Despite the benefits of mapping viral CAE and TAEs, methods to do so, especially for CAEs, tend to be laborious and/or highly technical, and traditionally focused on protein-coding sequences, rather than on regulatory sequences (27,28). Highly technical methods include multicolor longterm single-cell imaging (29), CRISPR/Cas9 deletion tiling (27,30), chemical probing approaches (31), targeted RNA mutagenesis and functional binding assays (32,33), and bioinformatics (6,34). Most methods, however, still rely on viral defective interfering (DI) RNAs, deducing critical genomic regions by serial passage.…”
Section: Introductionmentioning
confidence: 99%