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Updated: May 25, 2026
06:58
Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling
Published on: October 7, 2021
Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis
Marek Zywicki1, Kamilla Bakowska-Zywicka, Norbert Polacek
1Innsbruck Biocenter, Medical University Innsbruck, Division of Genomics and RNomics, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria. marek.zywicki@i-med.ac.at
Nucleic Acids Research
|January 24, 2012
Summary
Researchers developed APART, a novel computational pipeline for detecting RNA processing products from next-generation sequencing data. This tool identifies novel stable non-coding RNA (ncRNA) molecules and their processing events, aiding transcriptome research.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Current non-protein-coding RNA (ncRNA) transcriptome research primarily focuses on microRNA profiling and novel transcription unit detection.
- RNA processing is increasingly recognized as a multi-layer process generating diverse functional ncRNAs from single transcripts.
- A significant challenge in transcriptome research is the lack of methodologies to differentiate stable functional RNA species from transient degradation byproducts.
Purpose of the Study:
- To present APART, an automated computational pipeline for reliable detection of RNA processing products from next-generation sequencing data.
- To enable the assessment of widespread RNA processing events, a major obstacle in current transcriptome research.
- To identify novel stable ncRNA transcripts and processing products, and annotate known transcripts.
Main Methods:
- Development of an automated computational pipeline named APART.
- Implementation of efficient handling for non-unique sequencing reads.
- Integration of multiple data sources for transcript annotation.
- Analysis of a cDNA library from small ribosome-associated RNAs in Saccharomyces cerevisiae.
Main Results:
- APART successfully detected multiple novel stable RNA molecules.
- These novel RNAs were confirmed by independent experimental methods.
- The detected molecules were differentially processed from known ncRNAs (rRNAs, tRNAs, snoRNAs) in a stress-dependent manner.
- The pipeline demonstrated efficient handling of non-unique reads and annotation capabilities.
Conclusions:
- APART provides a complete workflow for reliable detection of RNA processing products from next-generation sequencing data.
- The pipeline facilitates the discovery of novel stable ncRNA species and processing events.
- APART aids in understanding the complexity of RNA processing and its role in cellular function, particularly under stress conditions.
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