Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing
| Autor: | Hoser, Simon M., Hoffmann, Anne, Meindl, Andreas, Gamper, Maximilian, Fallmann, Jörg, Bernhart, Stephan H., Müller, Lisa, Ploner, Melanie, Misslinger, Matthias, Kremser, Leopold, Lindner, Herbert, Geley, Stephan, Schaal, Heiner, Stadler, Peter F., Huettenhofer, Alexander |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
lcsh:QH426-470
RNA Splicing Alternative Splicing Constitutive Splicing Intronic Splicing Enhancer (ise) Mitochondrial Trna Nimtrna Numtdna Splicing Splicing Regulatory Element Trna Trna-lookalikes DNA Mutational Analysis RNA Transfer nimtRNA Humans RNA Messenger Constitutive splicing lcsh:QH301-705.5 tRNA Adaptor Proteins Signal Transducing Splicing regulatory element tRNA-lookalikes Research RNA-Binding Proteins Exons Introns Intronic splicing enhancer (ISE) Mitochondria DNA-Binding Proteins lcsh:Genetics lcsh:Biology (General) RNA Splice Sites Mitochondrial tRNA CRISPR-Cas Systems numtDNA |
| Zdroj: | Genome Biology Genome Biology, Vol 21, Iss 1, Pp 1-35 (2020) Genome Biol. 21:299 (2020) |
| ISSN: | 1474-760X 1474-7596 |
| Popis: | Background The presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. However, the biological roles of numtDNA remain elusive. Results Employing in silico analysis, we identify 281 mitochondrial tRNA homologs in the human genome, which we term nimtRNAs (nuclear intronic mitochondrial-derived tRNAs), being contained within introns of 76 nuclear host genes. Despite base changes in nimtRNAs when compared to their mtRNA homologs, a canonical tRNA cloverleaf structure is maintained. To address potential functions of intronic nimtRNAs, we insert them into introns of constitutive and alternative splicing reporters and demonstrate that nimtRNAs promote pre-mRNA splicing, dependent on the number and positioning of nimtRNA genes and splice site recognition efficiency. A mutational analysis reveals that the nimtRNA cloverleaf structure is required for the observed splicing increase. Utilizing a CRISPR/Cas9 approach, we show that a partial deletion of a single endogenous nimtRNALys within intron 28 of the PPFIBP1 gene decreases inclusion of the downstream-located exon 29 of the PPFIBP1 mRNA. By employing a pull-down approach followed by mass spectrometry, a 3′-splice site-associated protein network is identified, including KHDRBS1, which we show directly interacts with nimtRNATyr by an electrophoretic mobility shift assay. Conclusions We propose that nimtRNAs, along with associated protein factors, can act as a novel class of intronic splicing regulatory elements in the human genome by participating in the regulation of splicing. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-020-02199-6. |
| Databáze: | OpenAIRE |
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