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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

Project information

Project title:
Project's official title
Project's id
DFG KU3514/5-1
No information

Project financing: Deutsche Forschungsgemeinschaft
Elite Network of Bavaria University of Bayreuth

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.

Further data

Item Type: Article in a book
Refereed: Yes
Keywords: piRNAs; small RNAs; small RNA sequencing; bioinformatics; NGS analysis; automated pipeline; piRNAnalyzer; planarians
Institutions of the University: Faculties
Faculties > Faculty of Biology, Chemistry and Earth Sciences
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry VI - RNA Biochemistry
Profile Fields > Advanced Fields > Molecular Biosciences
Research Institutions > Central research institutes > Bayreuth Center for Molecular Biosciences - BZMB
Profile Fields
Profile Fields > Advanced Fields
Research Institutions
Research Institutions > Central research institutes
Result of work at the UBT: Yes
DDC Subjects: 500 Science
500 Science > 570 Life sciences, biology
Date Deposited: 23 Feb 2023 12:14
Last Modified: 30 Nov 2023 07:16