Age data is invaluable for all organisms, even those with known ages. For the unknowns, age data is essential for modelling work in the ecological/habitat management space. For the knowns, the gap between estimated and real age is a proxy for general health—accelerated aging rates imply poorer health, and vice versa.
Advances in epigenomics and sequencing have revealed that some cytosines exhibit age-specific changes in DNA methylation patterns. These markers, when assayed and processed with machine learning techniques, provide an age estimate: in non-model animals, this is a welcome alternative to destructive and cumbersome methods of age estimation e.g., fish otolith ring counting, coral coring.
Whilst there are existing epigenetic clocks for commercially relevant or model species e.g., humans, mice, whales and zebrafish, these clocks are species-specific and require a sequenced genome—there is a gap for a technique that works on non-charismatic animals, universally.
Here, we detail our initial efforts at exploring the methylation patterns of a well-conserved DNA loci across three animals: humans, zebrafish and prawns. These animals were chosen as they spanned the vertebrate/invertebrate and terrestrial/marine divides. We examined whether conservation of primary sequences was similarly reflected in the conservation of age-driven methylation patterns across organisms, and how the observations would ease calibration efforts of a pan-animal clock.
While preparing sequencing libraries, we experienced certain limitations linked to bisulphite conversion, the current gold standard for whole genome methylome investigations. We will share our experience on when (and when not) to rely on enzymatic conversion.