BACKGROUND POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF. RESULTS Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z. CONCLUSIONS We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.

中文翻译：

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POLG 中新的重叠编码序列的证据始于 CUG 起始密码子。

背景技术 POLG位于核染色体15上，编码DNA聚合酶γ(Pol γ)。Pol γ 负责线粒体 DNA (mtDNA) 的复制和修复。Pol γ 是大多数动物细胞线粒体中发现的唯一 DNA 聚合酶。POLG 突变是线粒体疾病最常见的单基因原因，已被定位在 POLG ORF 的编码区。结果使用 PhyloCSF 调查替代阅读框，我们在 POLG 的外显子 2 和 3 的替代框中发现了保守的编码特征，本文称为 ORF-Y，在胎盘哺乳动物中从头出现。使用 synplot2 程序，在与 ORF-Y 重叠的 POLG ORF 区域的哺乳动物中发现了同义位点保守。核糖体分析数据显示 ORF-Y 被翻译并且起始可能发生在 CUG 密码子处。对含有 ORF-Y 的哺乳动物序列的比对检查表明，CUG 密码子具有很强的起始背景，并且保守的预测 RNA 茎环从下游 14 个核苷酸开始。这些特征与近同源非 AUG 密码子的增强起始有关。Kim 等人的重新分析。(2014) 人类蛋白质组数据集草案产生了两种独特的肽，它们明确映射到 ORF-Y。在 POLG 的外显子 2 中还发现了一个额外的保守 uORF，本文称为 ORF-Z。最后，我们调查了与 POLG ORF 同义的 Clinvar 变体，发现这些变体中的大多数会导致 ORF-Y 或 ORF-Z 中的氨基酸变化。结论 我们为新的编码序列 ORF-Y 提供了证据，该序列与 POLG ORF 重叠。核糖体分析和质谱数据显示 ORF-Y 得到表达。PhyloCSF 和 synplot2 分析表明 ORF-Y 受到强烈的纯化选择。大量与疾病相关的突变映射到 POLG 的外显子 2 和 3，但也影响 ORF-Y，为这一发现提供了潜在的临床意义。