Let’s make a bet, you haven’t been to the zoo before!sncRNAs zoo!

A special study, from Chair for Clinical Bioinformatics, Saarland University, have developed a small noncoding RNAs (sncRNAs) repertoire database. SncRNAs in animals is considered to be evolutionarily conserved. Small noncoding RNAs and especially miRNAs are known to be expressed differently in organisms depending on various factors such as diseases, develop0mental stages or tissues. Therefore, the researchers want to find relationships between animal species and SncRNAs. They conducted low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Researchers evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. Researchers found that the distribution of sncRNAs in the different RNA classes varied significantly. The data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/.

The study have been published in the journal Nucleic Acids Research.

Background

For decades the main role of RNAs was believed to be either in the transfer of information between DNA and proteins (mRNAs) or in housekeeping functions (tRNAs, rRNAs). Because miRNAs have been described in a variety of organisms, their assumed conservation is frequently used to identify additional miRNAs in related species by homology- and sequence-based approaches. One of the most commonly performed types of study on sncRNAs is biomarker discovery analysis. It has already been demonstrated that the use of standardized protocols for collecting and analysing blood-borne miRNA profiles has huge potential for comparing biomarker profiles across different human pathologies.

sncRNAs zoo

Researchers collected 21 animal samples from regional zoos in Saarbr ¨ucken and Neunkirchen (Germany) comprising 19 different species, and created a phylogenetic tree of the animals. an online resource for the collected data was implemented and is freely available at: https://www.ccb.unisaarland.de/asra/. This resource provides access to all detected sncRNAs, their families and their expression patterns across all species in this study.

Results

One of the core hypotheses in this study is that the differences in read profiles between the species also mirror their known taxonomic classification. As expected, in almost all species, the most dominant read fraction is represented by rRNAs. However, the percentages vary substantially across species: from 7% in lynx to 49.3% in snowy owl, with a median of 35.2%. Researchers made use of three different miRNA databases with different scope: miRBase v22 (5), miRCarta v1.0 (6) and MirGeneDB 2.0.Zoo animals express common miRNA families that are more conserved than previously assumed. Gender and health condition have limited impact in crossspecies RNA expression.Some sncRNAs are processed depending on the superorder of their species.The results shows a stacked barplot for the number of recovered miRNAs deposited in the databases miRBase, miRCarta and MirGeneDB.

DATA AVAILABILITY

All sequencing data have been deposited in the Sequence Read Archive with the accession SRP162759.

Reference
Fehlmann T, Backes C, Pirritano M, et al. The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals[J]. Nucleic acids research, 2019, 47(9): 4431-4441.