Research Paper Volume 12, Issue 24 pp 24817—24835
A DNA methylation age predictor for zebrafish
- 1 Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia
- 2 Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
- 3 Western Australian Zebrafish Experimental Research Centre (WAZERC), University of Western Australia, Perth, Western Australia, Australia
- 4 School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
Received: October 14, 2020 Accepted: November 30, 2020 Published: December 23, 2020https://doi.org/10.18632/aging.202400
How to Cite
Copyright: © 2020 Mayne et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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 (Danio rerio), 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.