FishPi: a bioinformatic prediction tool to link piRNA and transposable elements in zebrafish

Abstract

Background: Piwi-interacting RNAs (piRNA)s are non-coding small RNAs that post-transcriptionally affect gene expression and regulation. Through complementary seed region binding with transposable elements (TEs), piRNAs protect the genome from transposition, and therefore a tool to link piRNAs with complementary TE targets is needed. Tools like TEsmall can process sRNA-seq datasets to produce differentially expressed piRNAs and piRScan developed for nematodes can link piRNAs and TEs but it requires the user to know the target region of interest and work backwards. Results: We have therefore developed FishPi to predict the pairings between piRNA and TEs. FishPi works with individual piRNAs or a list of piRNA sequences in fasta format. The software focuses on the piRNA:TE seed region and analyses reference TEs for piRNA complementarity. TE type is examined, counted and stored to a dictionary, with genomic loci recorded. Any updates to piRNA-TE binding rules, can easily be incorporated by updating the code underlying FishPi. FishPi provides a graphic interface, using tkinter, that requires the user to input piRNA sequences to generate comprehensive reports on piRNA:TE dynamics. FishPi can easily be adapted to other genomes opening the interpretation of piRNA functionality to a wide community. Conclusions: Users will gain insight into genome age and FishPi will help further our understanding of the biological role of piRNAs and their interaction with TEs in a similar way that public databases have improved the access to and the understanding of the role of small RNAs.