RNAcentral: a hub of information for non-coding RNA sequences

Sweeney, Blake A.; Petrov, Anton I.; Burkov, Boris; Finn, Robert D.; Bateman, Alex; Szymański, Maciej; Karłowski, Wojciech M.; Gorodkin, Jan; Seemann, Stefan E.; Cannone, Jamie J.; Gutell, Robin R.; Fey, Petra; Basu, Siddhartha; Kay, Simon; Cochrane, Guy; Billis, Konstantinos; Emmert, David B.; Marygold, Steven J; Huntley, Rachael P.; Lovering, Ruth C.; Frankish, Adam; Chan, Patricia P.; Lowe, Todd M.; Bruford, Elspeth A.; Seal, Ruth L.; Vandesompele, Jo; Volders, Pieter-Jan; Paraskevopoulou, Maria D.; Ma, Lina; Zhang, Zhang; Griffiths-Jones, Sam; Bujnicki, Janusz M.; Boccaletto, Pietro; Blake, Judith A.; Bult, Carol J.; Chen, Runsheng; Zhao, Yi; Wood, Valerie; Rutherford, Kim; Rivas, Elena; Cole, James R.; Laulederkind, Stanley J. F.; Shimoyama, Mary; Gillespie, Marc; Orlic-Milacic, M; Kalvari, Ioanna; Nawrocki, Eric P.; Engel, Stacia R.; Cherry, J. Michael; Team, Silva; Berardini, Tanya Z.; Hatzigeorgiou, Artemis G.; Karagkouni, Dimitra; Howe, Kevin; Davis, Paul A.; Dinger, Marcel E.; He, Shunmin; Yoshihama, Maki; Kenmochi, Naoya; Stadler, Peter F.; Williams, Kelly P.

doi:10.1093/nar/gky1034

Cited by 198 publications

(110 citation statements)

References 35 publications

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“…To investigate these conflicting hypotheses, we first curated a list of all nORFs that have been identified with evidence of translation. We obtained sequences for known and verified human proteins from NeXtProt ( https://www.nextprot.org/ ) 24 25 . While all the other datasets contained protein sequences whose translation has been experimentally verified in literature, the downloaded RNA central dataset contained 9,386,637 nucleotide transcript sequences.…”

mentioning

confidence: 99%

Proteins encoded by Novel ORFs have increased disorder but can be biochemically regulated and harbour pathogenic mutations

Jagannathan

Meena

Bhayankaram

et al. 2019

Preprint

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Recent advances in proteogenomics indicate that protein or protein-like products can be encoded by previously uncharacterized Open Reading Frames (ORFs) that we define as Novel Open Reading Frames (nORFs) 1 , 2 . Although it is yet unclear if these protein or protein-like products could possess any significant biological function hopes have been raised to target them for anticancer and antimicrobial therapy 3,4 . In this study, we used computational tools to systematically investigate these novel protein sequences for their propensities toward structural disorder, post-translational modifications (PTM) and mutational densities. We found that these novel proteins have significantly higher disorder and similar PTM frequencies compared to known proteins. Although these regions were found to harbour deleterious mutations, we did not observe any correlation between the pathogenicity of mutations and their location (ordered/disordered) within these novel proteins. This study suggests that these nORFs encode an important class of proteins, that could undergo sequence, structural or regulatory changes during complex diseases, and hence warrant further study. Significance:Certain noncoding regions of the genome are known to make protein-like products. These protein-like products have significantly expanded the number of the cellular proteome but we dont know whether they are capable of performing biological functions. Here in this study, we have investigated all such putative protein-like products and analyzed whether they can form structures, whether hey harbour mutations, and whether they can be regulated by biochemical regulatory processes. Results from this study indicate that indeed these protein-like proteins can perform and be involved in all the above processes.

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mentioning

confidence: 99%

Proteins encoded by Novel ORFs have increased disorder but can be biochemically regulated and harbour pathogenic mutations

Jagannathan

Meena

Bhayankaram

et al. 2019

Preprint

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“…First, data from QuickGO was mapped back to miRBase using RNAcentral [30]. NCBI Gene was used in conjunction with miRTarBase to produce the indirect annotations.…”

Section: Category Data Preprocessingmentioning

confidence: 99%

miEAA 2.0: Integrating multi-species microRNA enrichment analysis and workflow management systems

Kern

Fehlmann

Solomon

et al. 2020

Preprint

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AbstractGene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs.Here, we present miEAA 2.0, supporting miRNA input from Homo sapiens, Mus musculus, and Rattus norvegicus. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miR-Base miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualisations such as heatmaps and running sum curves with background distributions. Lastly, additional methods to correct for multiple hypothesis testing were implemented. We demonstrate the new features using case studies for human kidney cancer and mouse samples. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.

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“…The miRBase (v.22) mature and hairpin sequences were used as initial sequences resource. Via RNAcentral database [74], the cross-link between miRBase and Rfam (v.14.1) was retrieved, and a list of Rfam families were classified as annotated in both databases. In this case, by MIRFix the reported mature position was corrected along their corresponding hairpin sequence.…”

Section: Annotation Of Non-coding Rnasmentioning

confidence: 99%

The genome of the "Sea Vomit" Didemnum vexillum

Parra-Rincón¹,

Velandia-Huerto²,

Fallmann³

et al. 2020

Preprint

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Background: Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum is a colonial tunicate considered an invasive species with substantial ecological and economical risk.Results: We report a newly re-assembled genome of Didemnum vexillum. We used a hybrid approach that combines two genome sequencing technologies and also its first transcriptome. Started from 28.5 Gb Illumina and 12.35 Gb of PacBio data a new hybrid scaffolded assembly was obtained comprised of a total size of 517.55 Mb that increases contig length about 8-fold compared to previous, Illumina-only assembly. While still highly fragmented (L50=25284, N50=6539), the assembly is suffcient for comprehensive annotations of both protein-coding genes and non-coding RNAs.Conclusions: The draft assembly of the "sea vomit" genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.Availability: Genome and annotation data as well as a link to a UCSC Genome Browser hub are available at http://tunicatadvexillum.bioinf.uni-leipzig.de/.

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RNAcentral: a hub of information for non-coding RNA sequences

Cited by 198 publications

References 35 publications

Proteins encoded by Novel ORFs have increased disorder but can be biochemically regulated and harbour pathogenic mutations

Proteins encoded by Novel ORFs have increased disorder but can be biochemically regulated and harbour pathogenic mutations

miEAA 2.0: Integrating multi-species microRNA enrichment analysis and workflow management systems

The genome of the "Sea Vomit" Didemnum vexillum

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