tsRBase

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1. What are tsRNAs?

tRNA derived small RNAs (tsRNAs) that have been found in bacteria, yeast, plants and animals, are newly defined important functional small non-coding RNAs. Increasing evidence showed that tsRNAs are not random degradation products but generated by certain RNases cleavage of specific pre-tRNAs/mature tRNAs, and can regulate gene expression at transcriptional and/or post-transcriptional level.

2. What is in tsRBase?

tsRBase comprises tsRNA IDs, sequences, source tRNAs and expression value for tsRNAs observed in over 14000 samples from 20 different organisms, including Homo sapiens, Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Clostridium acetobutylicum, Danio rerio, Drosophila melanogaster, Escherichia coli, Gallus gallus, Glycine max, Mus musculus, Oryza sativa, Ovis aries, Physcomitrella patens, Rattus norvegicus, Schizosaccharomyces pombe, Sus scrofa, Vitis vinifera, Xenopus tropicalis and Zea mays. tsRBase collected and arranged information of tsRNAs with experimentally validated function and expression information by full-text mining on scientific papers to make tsRBase more comprehensive and systematic. Besides, tsRBase collects and exhibits tsRNA-target relations with high confidence from CLASH and CLEAR-CLIP data analysis.

3. Why use CLASH/CLEAR-CLIP data to explore tsRNA’s target?

Several studies reported that some tsRNAs could bind with Argonaute proteins and function as miRNAs, suppressing target gene expression at post-transcriptional level (PMID: 23297232, 27345152).
Crosslinking, ligation, and sequencing of hybrids (CLASH, below left, PMID: 23622248) and Covalent ligation of endogenous Argonaute-bound RNAs (CLEAR)-CLIP (below right, PMID: 26602609) are two new techniques that designed to directly observe in vivo miRNA-target interaction through AGO binding. Briefly, these techniques are similar to CLIP, but with the addition of a ligation step that connects the 3’ end of the AGO bound small RNA to the 5’ end of the target RNA. Furthermore, Kumar, Pankaj et al. found that human AGO1 CLASH data contains thousands of tsRNA reads chimeric with mRNA (PMID: 25270025). So we used a custom pipeline to explore tsRNA-target interaction in CLASH/CLEAR-CLIP data.

4. User guide

1)The pages and their utilities:

2)We provide three means for users to search tsRNAs, the picture shows the detail information:

3)The result list page:

4)The tsRNA detail information page: