A DNA methylation age predictor for zebrafish.

Area of Science:

• Epigenetics
• Comparative Genomics
• Vertebrate Biology

Background:

• DNA methylation patterns at CpG sites are established biomarkers for age prediction, primarily in mammals.
• Limited research exists on DNA methylation-based age estimation in non-mammalian vertebrates, particularly bony fish, the most diverse vertebrate class.
• Current genome-wide methods for DNA methylation analysis are expensive and not suitable for large-scale age estimation assays.

Purpose of the Study:

• To investigate the efficacy of DNA methylation changes for age prediction in zebrafish (Danio rerio).
• To develop a cost-effective and efficient assay for estimating fish age using DNA methylation.
• To explore the potential of DNA methylation as a broadly applicable aging biomarker in non-mammalian vertebrates.

Main Methods:

• Generated reduced representation bisulfite sequencing data from zebrafish caudal fin tissue across a range of ages (11.9–60.1 weeks).
• Identified specific CpG sites with age-correlated DNA methylation changes.
• Developed and validated a multiplex PCR assay using 26 optimized CpG sites for age prediction.

Main Results:

• Identified specific CpG sites in zebrafish whose methylation levels strongly correlate with chronological age.
• Developed a multiplex PCR assay capable of predicting zebrafish age with a median absolute error of 3.2 weeks (age range: 10.9–78.1 weeks).
• Demonstrated multiplex PCR as an efficient quantitative method for DNA methylation analysis in age estimation.

Conclusions:

• DNA methylation serves as a viable biomarker for age estimation in zebrafish, a model bony fish.
• The developed multiplex PCR assay offers an efficient and cost-effective alternative to genome-wide sequencing for age prediction.
• This study supports the broader application of DNA methylation-based aging methods in diverse non-mammalian vertebrate species.