School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia.
Genome Biol Evol. 2019 Jul 1;11(7):1883-1896. doi: 10.1093/gbe/evz132.
Several studies have linked mitochondrial genetic variation to phenotypic modifications; albeit the identity of the mitochondrial polymorphisms involved remains elusive. The search for these polymorphisms led to the discovery of small noncoding RNAs, which appear to be transcribed by the mitochondrial DNA ("small mitochondrial RNAs"). This contention is, however, controversial because the nuclear genome of most animals harbors mitochondrial pseudogenes (NUMTs) of identical sequence to regions of mtDNA, which could alternatively represent the source of these RNAs. To discern the likely contributions of the mitochondrial and nuclear genome to transcribing these small mitochondrial RNAs, we leverage data from six vertebrate species exhibiting markedly different levels of NUMT sequence. We explore whether abundances of small mitochondrial RNAs are associated with levels of NUMT sequence across species, or differences in tissue-specific mtDNA content within species. Evidence for the former would support the hypothesis these RNAs are primarily transcribed by NUMT sequence, whereas evidence for the latter would provide strong evidence for the counter hypothesis that these RNAs are transcribed directly by the mtDNA. No association exists between the abundance of small mitochondrial RNAs and NUMT levels across species. Moreover, a sizable proportion of transcripts map exclusively to the mtDNA sequence, even in species with highest NUMT levels. Conversely, tissue-specific abundances of small mitochondrial RNAs are strongly associated with the mtDNA content. These results support the hypothesis that small mitochondrial RNAs are primarily transcribed by the mitochondrial genome and that this capacity is conserved across Amniota and, most likely, across most metazoan lineages.
几项研究将线粒体遗传变异与表型修饰联系起来；尽管涉及的线粒体多态性的身份仍然难以捉摸。对这些多态性的研究导致了小非编码 RNA 的发现，这些 RNA 似乎由线粒体 DNA（“小线粒体 RNA”）转录。然而，这种说法存在争议，因为大多数动物的核基因组都含有与 mtDNA 区域相同序列的线粒体假基因（NUMTs），这些 RNA 可能是这些假基因的来源。为了区分线粒体和核基因组对转录这些小线粒体 RNA 的可能贡献，我们利用来自六个表现出明显不同 NUMT 序列水平的脊椎动物物种的数据。我们探讨了小线粒体 RNA 的丰度是否与物种间 NUMT 序列的水平相关，或者是否与物种内组织特异性 mtDNA 含量的差异相关。前者的证据将支持这些 RNA 主要由 NUMT 序列转录的假设，而后者的证据将为这些 RNA 直接由 mtDNA 转录的反假设提供强有力的证据。小线粒体 RNA 的丰度与物种间的 NUMT 水平之间没有关联。此外，即使在 NUMT 水平最高的物种中，相当一部分转录本也仅映射到 mtDNA 序列。相反，小线粒体 RNA 的组织特异性丰度与 mtDNA 含量强烈相关。这些结果支持小线粒体 RNA 主要由线粒体基因组转录的假设，并且这种能力在羊膜动物中是保守的，很可能在大多数后生动物谱系中也是保守的。
