Non‐Coding RNA Analysis Using the Rfam Database

Kalvari, Ioanna; Nawrocki, Eric P.; Argasinska, Joanna; Quinones-Olvera, Natalia; Finn, Robert D.; Petrov, Anton I.

doi:10.1002/cpbi.51

Cited by 339 publications

(257 citation statements)

References 20 publications

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“…Local regions of highly negative z-scores and MFE values are found throughout the entirety of the genome and do not immediately appear concentrated in any given genomic region. However, two known RNA structural motifs annotated for human coronaviruses in Rfam 14,15 overlapped regions predicted with negative z-scores: SL1-2 and the FSE ( Fig. 1c and 1d ).…”

Section: Resultsmentioning

confidence: 97%

Anin silicomap of the SARS-CoV-2 RNA Structurome

Andrews

Haniff

et al. 2020

Preprint

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SARS-CoV-2 is a positive-sense single-stranded RNA virus that has exploded throughout the global human population. This pandemic coronavirus strain has taken scientists and public health researchers by surprise and knowledge of its basic biology (e.g. structure/function relationships in its genomic, messenger and template RNAs) and modes for therapeutic intervention lag behind that of other human pathogens. In this report we used a recently-developed bioinformatics approach, ScanFold, to deduce the RNA structural landscape of the SARS-CoV-2 transcriptome. We recapitulate known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that the SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a huge reservoir of potential drug targets for RNA-binding small molecules. Our results also predict regions that are accessible for intermolecular interactions, which can aid in the design of antisense therapeutics. All results are made available via a public database (the RNAStructuromeDB) where they may hopefully drive drug discovery efforts to inhibit SARS-CoV-2 pathogenesis. Δ G° z-score region is the 3′UTR, which was found to yield mostly positive z-scores; despite a higher than average GC content for this region (0.45 on average; Table S1), MFE values here were less stable than expected, averaging Δ G° z-scores of +0.98 (or roughly one standard deviation less stable than random). Scans were also performed in the negative sense of the genome, revealing slightly less propensity for structure. The MFE values ranged from -42.9 to -6.0 and averaged -23.25 kcal/mol; z-scores in the negative sense had a similar range of Δ G° z-scores as the positive sense (-5.76 to 2.66) but averaged lower at -1.12 (Table S1). Interestingly, Δ G° z-scores for the 3′ UTR in negative sense were more skewed to the negative (finding minimums as low as -2.32) resulting in an average z-score of 0.16 for the region.

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Section: Resultsmentioning

confidence: 97%

Anin silicomap of the SARS-CoV-2 RNA Structurome

Andrews

Haniff

et al. 2020

Preprint

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“…Adapters were removed using Trim Galore (Krueger, 2012) when necessary, with options -length 10, and --quality 20. Following trimming, structural and noncoding RNAs, and reads mapping to the A. thaliana chloroplast or mitochondria genomes, were removed by aligning to the rfam database v14 (Kalvari et al, 2018a(Kalvari et al, , 2018b, excluding miRNAs and miRNA precursors, and the TAIR10 (Berardini et al, 2015) chloroplast and mitochondrial genomes using Bowtie (Langmead et al, 2009). Following these steps, reads shorter than 19 nt and longer than 26 nt were removed with a Python script (fastq_length_filter.py).…”

Section: Small Rna Sequencing and Analysismentioning

confidence: 99%

Abundant expression of maternal siRNAs is a conserved feature of seed development

Grover

Burgess

Kendall

et al. 2019

Preprint

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Small RNAs are abundant in plant reproductive tissues, especially 24-nt short interfering (si)RNAs. Most 24-nt siRNAs are dependent on RNA Pol IV and RDR2, and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa, RdDM is required in the maternal sporophyte for successful seed development. Here we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during B. rapa seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in diverse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.

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“…Homologous genes were recovered using BLAST+ blastp (Camacho et al 2009), with alignment coverage >80%, identity percentage > 80% and an e-value threshold of 1e-10. Rfam release 13 (Nawrocki et al 2015) and Infernal v1.1.1 (Nawrocki and Eddy 2013) were used for the annotation of non-coding genes as it was previously described (Kalvari et al 2018). For tRNAs, tRNAscan-SE v.1.3.1 (Lowe and Chan 2016) was used with the euakyotic model.…”

Section: Discussionmentioning

confidence: 99%

Nanopore sequencing significantly improves genome assembly of the eukaryotic protozoan parasite Trypanosoma cruzi

Díaz-Viraqué

Pita

Greif

et al. 2018

Preprint

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Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a two-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given that half of its genome is composed of repetitive sequences. Here, we report de novo assemblies, annotation and comparative analyses of the Berenice strain using a combination of Illumina short reads and MinION long reads. Our work demonstrates that Nanopore sequencing improves T. cruzi assembly contiguity and increases the assembly size in ~16Mb. Specifically, we found that assembly improvement also refines the completeness of coding regions for both single copy genes and repetitive transposable elements. Beyond its historical and epidemiological importance, Berenice constitutes a fundamental resource since it now represents the best-quality assembly available for TcII, a highly prevalent lineage causing human infections in South America. The availability of Berenice genome expands the known genetic diversity of T. cruzi and facilitates more comprehensive evolutionary inferences. Our work represents the first report of Nanopore technology used to resolve complex protozoan genomes, supporting its subsequent application for improving trypanosomatid and other highly repetitive genomes. 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

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Non‐Coding RNA Analysis Using the Rfam Database

Cited by 339 publications

References 20 publications

Anin silicomap of the SARS-CoV-2 RNA Structurome

Anin silicomap of the SARS-CoV-2 RNA Structurome

Abundant expression of maternal siRNAs is a conserved feature of seed development

Nanopore sequencing significantly improves genome assembly of the eukaryotic protozoan parasite Trypanosoma cruzi

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