Abstract
Mitochondrial DNA (mtDNA) heteroplasmies are associated with various diseases but the transmission of heteroplasmy from mtDNA to mitochondrial RNA (mtRNA) remains unclear. We compared heteroplasmies in mtRNA from 446 human B-lymphoblastoid cell lines to their corresponding mtDNA using deep sequencing data from two independent studies. We observed 2786 heteroplasmies presenting in both DNA and RNA at 1% frequency cutoff. Among them, the frequencies of 2427 (87.1%) heteroplasmies were highly consistent (less than 5% frequency difference) between DNA and RNA. To validate these frequency consistencies, we isolated DNA and RNA simultaneously from GM12282 cell line used in those two sequencing studies, and resequenced its heteroplasmy sites. Interestingly, we also observed the rapid changes of heteroplasmy frequencies during 4 weeks of the cell culture: the frequencies at Day 14 increased by >25% than those at Day 0. However, the heteroplasmy frequencies from the same time point were highly consistent. In summary, our analysis on public data together with in vitro study indicates that the heteroplasmies in DNA can be transcribed into RNA with high fidelity. Meanwhile, the observed rapid-changing heteroplasmy frequency can potentially disturb cell functions, which could be an overlooked confounding factor in cell line related studies.
Highlights
The genetic information from DNA needs to be transcribed to RNA for protein synthesis to achieve biological functions
We investigated whether the extensively existing heteroplasmic variations in mitochondrial DNA (mtDNA) were observable in mitochondrial RNA (mtRNA), whether the heteroplasmy frequencies presented in RNA would keep consistent with that in DNA
The sequencing reads were first aligned to human reference genome hg[19], and after a series of quality control steps, we retained high quality mtDNA sequencing reads for subsequent mitochondrial heteroplasmy analysis (Methods)
Summary
The genetic information from DNA needs to be transcribed to RNA for protein synthesis to achieve biological functions. There are few studies to investigate the transmission of mtDNA heteroplasmies to mitochondrial RNA (mtRNA). It remains unclear whether mutated and wild type mtDNA are transcribed proportionally. We comprehensively analyzed 446 pairs of RNA and DNA sequences from human lymphoblastoid cell lines, which were a subset of individuals from 1000 genome project[14,15]. We investigated whether the extensively existing heteroplasmic variations in mtDNA were observable in mtRNA, whether the heteroplasmy frequencies presented in RNA would keep consistent with that in DNA. Our results demonstrated that the majority of heteroplasmies in mitochondrial DNA (mtDNA) could be transcribed proportionally to RNA regardless of their pathogenic degrees. During the cell culture process, we observed that the heteroplasmies frequencies were changing dramatically with time which may disturb the cellular functions according to the mtDNA heteroplasmy threshold effects
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