Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper-resistance gene CUP1. Transcription of the tandemly repeated CUP1 gene causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. We have developed a sensitive and quantitative eccDNA sequencing pipeline that reveals CUP1 eccDNA accumulation on copper exposure to be exquisitely site specific, with no other detectable changes across the eccDNA complement. eccDNA forms de novo from the CUP1 locus through processing of DNA double-strand breaks (DSBs) by Sae2, Mre11 and Mus81, and genome-wide analyses show that other protein coding eccDNA species in aged yeast share a similar biogenesis pathway. Although abundant, we find that CUP1 eccDNA does not replicate efficiently, and high-copy numbers in aged cells arise through frequent formation events combined with asymmetric DNA segregation. The transcriptional stimulation of CUP1 eccDNA formation shows that age-linked genetic change varies with transcription pattern, resulting in gene copy number profiles tailored by environment.

中文翻译：

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酵母老化过程中转录诱导的染色体外 DNA 形成。

染色体外环状 DNA (eccDNA) 通过允许快速和广泛的基因拷贝数变异促进适应性进化，并与癌症和衰老的病理学有关。在这里，我们证明在环境铜环境下老化的酵母会积累高水平的含有铜抗性基因 CUP1 的 eccDNA。串联重复的 CUP1 基因的转录导致 CUP1 eccDNA 积累，这发生在没有表型选择的情况下。我们开发了一种灵敏且定量的 eccDNA 测序管道，揭示了铜暴露时 CUP1 eccDNA 的积累具有精确的位点特异性，在 eccDNA 补体中没有其他可检测的变化。eccDNA 通过 Sae2、Mre11 和 Mus81 处理 DNA 双链断裂 (DSB) 从 CUP1 基因座重新形成，和全基因组分析表明，老化酵母中的其他蛋白质编码 eccDNA 物种具有相似的生物发生途径。虽然丰富，但我们发现 CUP1 eccDNA 不能有效复制，并且衰老细胞中的高拷贝数是通过频繁的形成事件与不对称 DNA 分离相结合而产生的。CUP1 eccDNA 形成的转录刺激表明，与年龄相关的遗传变化随转录模式而变化，导致基因拷贝数分布因环境而异。