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

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Piwi-interacting RNAs (piRNAs) are small non-coding RNAs crucial for genome defense against transposable elements (TEs).
• Understanding piRNA-TE interactions is key to comprehending genome maintenance and gene regulation.
• Existing tools have limitations in linking piRNAs to their specific TE targets across diverse species.

Purpose of the Study:

• To develop a user-friendly tool, FishPi, for predicting piRNA-TE interactions.
• To facilitate the analysis of piRNA complementarity with TEs in various genomes.
• To enhance the study of piRNA function in genome stability.

Main Methods:

• FishPi analyzes piRNA sequences against reference TEs, focusing on the seed region for complementarity.
• The tool allows user customization of parameters such as piRNA orientation and mismatches.
• It processes individual piRNAs or lists in FASTA format and generates scored piRNA-TE match reports.

Main Results:

• FishPi successfully predicts piRNA-TE pairings for zebrafish, medaka, and tilapia genomes.
• The software identifies TE types, counts them, and records genomic loci of interactions.
• A graphical user interface (GUI) simplifies input and report generation for piRNA-TE interactions.

Conclusions:

• FishPi provides valuable insights into genome mobility by identifying piRNA-TE interactions.
• The tool aids in understanding the biological roles of piRNAs in genome maintenance.
• FishPi's adaptability to new genomes broadens the interpretation of piRNA functionality for the research community.