Related Experiment Video
Updated: Aug 16, 2025
06:37
Ubiquitous and Tissue-specific RNA Targeting in Drosophila Melanogaster using CRISPR/CasRx
Published on: February 5, 2021
3.2K
Transcriptome-wide analysis of pseudouridylation in Drosophila melanogaster
Wan Song1,2, Ram Podicheti3, Douglas B Rusch3
1Gill Center for Biomolecular Research, Indiana University, Bloomington, IN 47405, USA.
G3 (Bethesda, Md.)
|December 19, 2022
Summary
Researchers optimized RNA pseudouridine (Psi) detection in Drosophila melanogaster, finding thousands of Psi modifications across the transcriptome. This study highlights Psi
Area of Science:
- Molecular Biology
- Genomics
- RNA Biology
Background:
- Pseudouridine (Psi) is a prevalent RNA modification found across various RNA types, including mRNA, rRNA, and non-coding RNAs.
- Understanding Psi distribution and function is crucial for comprehending gene regulation and cellular processes.
- Previous transcriptome-wide Psi detection (Psi-seq) had not been established for the model organism Drosophila melanogaster.
Purpose of the Study:
- To optimize and implement Psi-seq for transcriptome-wide pseudouridine profiling in Drosophila melanogaster.
- To identify and characterize pseudouridine modification sites in the female fly head transcriptome.
- To investigate the role of pseudouridylation in ribosomal and mitochondrial function, and identify potential targets of the RluA-2 enzyme.
Main Methods:
- Optimization of the Psi-seq protocol for Drosophila melanogaster.
- High-throughput sequencing to map pseudouridine modifications across the transcriptome.
- Comparative analysis between RluA-2 mutant and control (w1118) genotypes.
- Differential gene expression analysis.
Main Results:
- Thousands of pseudouridine modification sites were identified throughout the female fly head transcriptome.
- Pseudouridine modifications are widespread in both cellular and mitochondrial rRNAs, and over a thousand sites were found on mRNAs.
- Genes encoding ribosomal proteins and mitochondrial RNAs are frequently pseudouridylated.
- The 7SLRNA and yolk protein mRNAs (Yp1, Yp2, Yp3) were identified as highly enriched for pseudouridine.
- Several pseudouridine sites were found to be missing in the RluA-2 mutant, suggesting they are RluA-2 targets.
- Loss of RluA-2 significantly impacts the ribosome and translational machinery.
Conclusions:
- The optimized Psi-seq method enables comprehensive pseudouridine profiling in Drosophila melanogaster.
- Pseudouridylation plays a significant role in ribosome biogenesis, mitochondrial function, and translational regulation in flies.
- RluA-2 is implicated as a key enzyme in pseudouridine modification with broad effects on the transcriptome and translational machinery.
