Abstract
BackgroundThe abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Nevertheless, many aspects are still unclear, specifically about the variability of the 22 human mitochondrial transfer RNA (tRNA) genes and their involvement in diseases. The complex enrichment and isolation of tRNAs in vitro leads to an incomplete knowledge of their post-transcriptional modifications and three-dimensional folding, essential for correct tRNA functioning. An accurate annotation of mitochondrial tRNA variants would be definitely useful and appreciated by mitochondrial researchers and clinicians since the most of bioinformatics tools for variant annotation and prioritization available so far cannot shed light on the functional role of tRNA variations.ResultsTo this aim, we updated our MToolBox pipeline for mitochondrial DNA analysis of high throughput and Sanger sequencing data by integrating tRNA variant annotations in order to identify and characterize relevant variants not only in protein coding regions, but also in tRNA genes. The annotation step in the pipeline now provides detailed information for variants mapping onto the 22 mitochondrial tRNAs. For each mt-tRNA position along the entire genome, the relative tRNA numbering, tRNA type, cloverleaf secondary domains (loops and stems), mature nucleotide and interactions in the three-dimensional folding were reported. Moreover, pathogenicity predictions for tRNA and rRNA variants were retrieved from the literature and integrated within the annotations provided by MToolBox, both in the stand-alone version and web-based tool at the Mitochondrial Disease Sequence Data Resource (MSeqDR) website. All the information available in the annotation step of MToolBox were exploited to generate custom tracks which can be displayed in the GBrowse instance at MSeqDR website.ConclusionsTo the best of our knowledge, specific data regarding mitochondrial variants in tRNA genes were introduced for the first time in a tool for mitochondrial genome analysis, supporting the interpretation of genetic variants in specific genomic contexts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1193-4) contains supplementary material, which is available to authorized users.
Highlights
The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics
Thanks to the “four-way wobble rule” and post transcriptional modifications at the first letters of transfer RNA (tRNA) anticodons [2], only 22 mitochondrial transfer RNAs (mt-tRNA) are sufficient in humans, as well as in other mammals, to translate all sense codons into 13 subunits of respiratory chain complexes encoded in each single copy of mitochondrial DNA (mtDNA) [2]. mt-tRNAs could be considered hot spots of mutations [3]: among more than 600 disease associated mutations compiled to date, about 240 were mapped on mt-tRNA genes [4]
New fields were added in the latest version of the MToolBox pipeline (Table 1): specific annotations for tRNA and rRNA genes, annotations from ClinVar database for disease-associated variants [26] and conservation scores for each site produced by PhyloP [21] and PhastCons [22] algorithms
Summary
The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Many aspects are still unclear, about the variability of the 22 human mitochondrial transfer RNA (tRNA) genes and their involvement in diseases. Thanks to the “four-way wobble rule” and post transcriptional modifications at the first letters of tRNA anticodons [2], only 22 mt-tRNAs are sufficient in humans, as well as in other mammals, to translate all sense codons into 13 subunits of respiratory chain complexes encoded in each single copy of mtDNA [2]. Post-transcriptional modifications by nuclear-encoded enzymes [7, 8] often occur in key positions for a correct tRNA functioning, including folding and codon-anticodon interaction [6, 9, 10]. The lack of a correct post-transcriptional process could cause pathological effects [11, 12]
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