Genome-wide analysis of planarian piRNAs

Title data

Pittroff, Andreas ; Kim, Iana ; Kuhn, Claus-D.:
Genome-wide analysis of planarian piRNAs.
In: Gentile, Luca (ed.): Schmidtea Mediterranea : Methods and Protocols. - New York : Humana Press , 2023 . - pp. 55-65 . - (Methods in Molecular Biology ; 2680 )
ISBN 978-1-0716-3275-8
DOI: https://doi.org/10.1007/978-1-0716-3275-8_3

Project information

Abstract in another language

In planarian flatworms, the piRNA pathway is operated by three PIWI proteins, termed SMEDWI-1, -2 and -3 (SMEDWI = Schmidtea mediterranea PIWI). The interplay between these three PIWI proteins and their associated small non-coding RNAs, termed piRNAs, fuels the outstanding regenerative abilities of planarians, enables tissue homeostasis and, ultimately, ensures animal survival. As the molecular targets of PIWI proteins are determined by the sequences of their co-bound piRNAs, it is imperative to identify these sequences by next-generation sequencing applications. Following sequencing, the genomic targets and the regulatory potential of the isolated piRNA populations need to be uncovered. To that end, here we present a bioinformatics analysis pipeline for processing and systematic characterization of planarian piRNAs. The pipeline includes steps for the removal of PCR duplicates based on unique molecular identifier (UMI) sequences, and it accounts for piRNA multimapping to different loci in the genome. Importantly, our protocol also includes a fully automated pipeline that is freely available at Github. Together with the piRNA isolation and library preparation protocol (see accompanying chapter), the presented computational pipeline enables researchers to explore the functional role of the piRNA pathway in flatworm biology.