Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia.
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia.
Aging (Albany NY). 2020 Dec 23;12(24):24817-24835. doi: 10.18632/aging.202400.
Changes in DNA methylation at specific CpG sites have been used to build predictive models to estimate animal age, predominantly in mammals. Little testing for this effect has been conducted in other vertebrate groups, such as bony fish, the largest vertebrate class. The development of most age-predictive models has relied on a genome-wide sequencing method to obtain a DNA methylation level, which makes it costly to deploy as an assay to estimate age in many samples. Here, we have generated a reduced representation bisulfite sequencing data set of caudal fin tissue from a model fish species, zebrafish (), aged from 11.9-60.1 weeks. We identified changes in methylation at specific CpG sites that correlated strongly with increasing age. Using an optimised unique set of 26 CpG sites we developed a multiplex PCR assay that predicts age with an average median absolute error rate of 3.2 weeks in zebrafish between 10.9-78.1 weeks of age. We also demonstrate the use of multiplex PCR as an efficient quantitative approach to measure DNA methylation for the use of age estimation. This study highlights the potential further use of DNA methylation as an age estimation method in non-mammalian vertebrate species.
特定 CpG 位点的 DNA 甲基化变化已被用于构建预测模型，以估计动物的年龄，主要是在哺乳动物中。在其他脊椎动物群体（如骨鱼，最大的脊椎动物类群）中，对这种影响的测试很少。大多数年龄预测模型的开发都依赖于全基因组测序方法来获得 DNA 甲基化水平，这使得在许多样本中作为估计年龄的检测方法部署成本很高。在这里，我们从模式鱼类斑马鱼（）生成了尾鳍组织的代表性双碱基测序数据集，其年龄从 11.9 周到 60.1 周不等。我们确定了特定 CpG 位点的甲基化变化，这些变化与年龄的增加密切相关。使用优化的 26 个 CpG 位点的独特集合，我们开发了一种多重 PCR 测定法，可在 10.9-78.1 周龄的斑马鱼中预测年龄，平均中位数绝对误差率为 3.2 周。我们还证明了多重 PCR 作为一种有效的定量方法，可用于测量用于年龄估计的 DNA 甲基化。本研究强调了在非哺乳动物脊椎动物物种中进一步将 DNA 甲基化用作年龄估计方法的潜力。
