If time drags and money disappears when looking at DNA methylation-based epigenetic clocks, you are “in time” to hear of a newly described efficient and cost-effective bisulfite sequencing approach! Time flies – but money does not – with “tagmentation-based indexing for methylation sequencing” or TIME-seq!
An on-time team led by David A. Sinclair (Harvard Medical School) knew of the difficulties facing the broader application of DNA methylation-based epigenetic clocks. To this end, they developed TIME-seq to measure a minimal number of age-correlated loci and keep reagent use and sequencing/labor costs low to make construction more manageable. Applying short, barcoded, sodium bisulfite-resistant Tn5 transposase adaptors to index sample DNA for pooled library preparation streamlines the protocol and minimizes costs. An optimized in-solution hybridization enrichment steps use biotinylated RNA baits for deep coverage with minimal sequencing costs, with Illumina short-read sequencing following bisulfite conversion of DNA and indexed PCR amplification of pools, with sample reads demultiplexed via pool/Tn5 adapter indexes.
Let’s hear from Griffen and colleagues on how TIME-seq “flies” when constructing cost-effective epigenetic clocks:
- Assaying DNA methylation at ~1000 CpG islands with elevated age correlations (from previsouly reported blood and multi-tissue clocks) helps to construct multi-tissue/tissue-specific mouse epigenetic clocks using TIME-seq
- Analysis of thousands of DNA samples from multiple tissues involves a cost of ~$6 (USD) per sample
- The multi-tissue epigenetic clock accurately predicts age (error of ~2 months), while the various tissue-specific epigenetic clocks also displayed high accuracy (error of 0.95-1.98 months)
- TIME-seq becomes increasingly economical at scale, potentially reaching a cost of ~$2 per sample
- Encouragingly, mouse epigenetic clocks developed using TIME-seq detect induced differences in biological aging after the application of specific interventions aimed at modulating this process
- Calorific restriction decelerates aging and a high-fat diet accelerates aging according to mouse blood and liver epigenetic clocks, while epigenetic rejuvenation in the liver thanks to the forced expression of Oct-4, Sox-2, and Klf-4 winds back the multi-tissue epigenetic clock to a younger predicted age
- Finally, TIME-seq supports the straightforward development of cost-effective, highly-accurate human epigenetic clocks
- Construction uses over 1000 blood DNA samples from human donors aged 18 to 103 and age-correlated loci to assay DNA methylation at ~10,000 CpGs at a cost of ~$6 per sample
- The human blood epigenetic clock provides accurate predictions with an error of ~3 years
Epigenetic clocks can take a week to construct using a complex workflow at a price of $30–50 per sample; however, TIME-seq may decrease cost by two orders of magnitude and let you process ~800 samples in less than two days without automation. However, future automation could support the lower-cost analysis of countless thousands of samples from vast cohorts and enable cheaper and more efficient DNA methylation-based epigenetic age measurement in larger-scale human and animal studies. Let’s hope that TIME-seq really does fly!
For more on how time flies when constructing cost-effective, accurate epigenetic clocks, see Nature Aging, January 2024.