ArticleNucleic acids research2012
Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
36 citing papers in PubMed, 60 citations in OpenAlex.
- Transfer RNA-derived small RNAs (tsRNAs): A rising star in liquid biopsy.Genes & diseases · 2025Review
- tDR-quant: a reliable electroporation-based approach for quantifying tRNA-derived fragments binding to ribosomes.FEMS yeast research · 2025Article
- Review
- tRNA renovatio: Rebirth through fragmentation.Molecular cell · 2023Review
- Current Status of Regulatory Non-Coding RNAs Research in the Tritryp.Non-coding RNA · 2022Review
- Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes.Non-coding RNA · 2022Review
- MiR-590-5p inhibits pathological hypertrophy mediated heart failure by targeting RTN4.Journal of molecular histology · 2021Article
- Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs.Non-coding RNA · 2021Review
- Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs inInternational journal of molecular sciences · 2021Article
- Diversification of piRNAs expressed in PGCs and somatic cells during embryonic gonadal development.RNA biology · 2020Article
- Modulation of mammalian translation by a ribosome-associated tRNA half.RNA biology · 2020Article
- Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression.Scientific reports · 2019Article
- A tRNA half modulates translation as stress response in Trypanosoma brucei.Nature communications · 2019Article
- Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z.EMBO reports · 2018Article
- mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii.Scientific reports · 2018Article
- Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues.PloS one · 2018Article
- Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease.RNA (New York, N.Y.) · 2017Article
- The widespread occurrence of tRNA-derived fragments inFEBS open bio · 2016Article
- tRNA-derived short RNAs bind to Saccharomyces cerevisiae ribosomes in a stress-dependent manner and inhibit protein synthesis in vitro.FEMS yeast research · 2016Article
- Transfer RNA Derived Small RNAs Targeting Defense Responsive Genes Are Induced during Phytophthora capsici Infection in Black Pepper (Piper nigrum L.).Frontiers in plant science · 2016Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The exploration of the non-protein-coding RNA (ncRNA) transcriptome is currently focused on profiling of microRNA expression and detection of novel ncRNA transcription units. However, recent studies suggest that RNA processing can be a multi-layer process leading to the generation of ncRNAs of diverse functions from a single primary transcript. Up to date no methodology has been presented to distinguish stable functional RNA species from rapidly degraded side products of nucleases. Thus the correct assessment of widespread RNA processing events is one of the major obstacles in transcriptome research. Here, we present a novel automated computational pipeline, named APART, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data. The major features include efficient handling of non-unique reads, detection of novel stable ncRNA transcripts and processing products and annotation of known transcripts based on multiple sources of information. To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. By employing the APART pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable RNA molecules differentially processed from well known ncRNAs, like rRNAs, tRNAs or snoRNAs, in a stress-dependent manner.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.