Journal Article

Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing

Hoffmann, Anne, Schaal, Heiner, Geley, Stephan, Kremser, Leopold, Hoser, Simon M., Meindl, Andreas, Misslinger, Matthias, Fallmann, Jörg, Gamper, Maximilian, Ploner, Melanie, Huettenhofer, Alexander, Müller, Lisa, Stadler, Peter F., Bernhart, Stephan H., Lindner, Herbert

2020

Overview

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 nimtRNA Lys 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 nimtRNA Tyr 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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Adaptor Proteins, Signal Transducing - genetics / Alternative Splicing / Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / class / computer simulation / CRISPR / CRISPR-Cas Systems / Deoxyribonucleic acid / DNA / DNA Mutational Analysis / DNA-Binding Proteins - genetics / Electrophoretic mobility / Enzymes / Evolutionary Biology / Exons / gel electrophoresis / Gene expression / Genomes / Human Genetics / Humans / Intronic splicing enhancer (ISE) / Introns / Life Sciences / Mammals / mass spectrometry / Mass spectroscopy / Microbial Genetics and Genomics / MicroRNAs / mitochondria / Mitochondria - genetics / Mitochondrial DNA / mRNA / mutational analysis / nimtRNA / numtDNA / Plant Genetics and Genomics / Proteins / Regulatory sequences / RNA polymerase / RNA Splice Sites / RNA Splicing / RNA, Messenger / RNA, Transfer - genetics / RNA, Transfer - metabolism / RNA-Binding Proteins - genetics / Splicing regulatory element / tRNA / tRNA-lookalikes