A novel understanding of global DNA methylation in bobcat (<i>Lynx rufus</i>)

Cantrell, Bonnie; Friedman, Sydney R.; Lachance, Hannah; Bernier, Chris; Murdoch, Brenda M.; Frattini, S.; Talenti, Andrea; Crepaldi, P.; McKay, Stephanie

doi:10.1139/gen-2019-0046

Cited by 4 publications

(5 citation statements)

References 31 publications

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“…Currently the most common method for global DNA methylation uses a colorimetric antibody based commercial ELISA kit, which suffers from poor resolution with small magnitude differences and poor repeatability overall. 28 Further, it only measures the methylated cytosine to total cytosine ratio, making its relation to cytosines in CpG context difficult to interpret.…”

Section: Discussionmentioning

confidence: 99%

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Faulk

2023

Preprint

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Genome skimming is defined as low-pass sequencing below 0.05X coverage and is typically used for mitochondrial genome recovery and species identification. Long read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001X, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole genome bisulfite sequencing and an average mapping rate above 97%. Genome size directly correlates to global DNA methylation, explaining 44% of its variance. Accurate SINE and LINE transposon methylation in both mouse and primates can be obtained with just 0.0001X coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology, and by low resource groups.

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Section: Discussionmentioning

confidence: 99%

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Faulk

2023

Preprint

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“…Currently the most common method for global DNA methylation uses a colorimetric antibody-based commercial ELISA kit, which suffers from poor resolution with small-magnitude differences and poor repeatability overall ( Cantrell et al 2020 ). Further, it only measures the methylated cytosine–to–total cytosine ratio, making its relation to cytosines in CpG context difficult to interpret.…”

Section: Discussionmentioning

confidence: 99%

“…Detection range and accuracy are confirmed by repeated measures of the technical replicate control samples. Biological replication is validated by highly consistent interindividual measurements Currently the most common method for global DNA methylation uses a colorimetric antibody-based commercial ELISA kit, which suffers from poor resolution with small-magnitude differences and poor repeatability overall (Cantrell et al 2020). Further, it only measures the methylated cytosine-to-total cytosine ratio, making its relation to cytosines in CpG context difficult to interpret.…”

Section: Discussionmentioning

confidence: 99%

Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates

Faulk

2023

Genome Res.

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Genome skimming is defined as low-pass sequencing below 0.05× coverage and is typically used for mitochondrial genome recovery and species identification. Long-read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001×, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole-genome bisulfite sequencing and an average mapping rate >97%. Genome size directly correlates to global DNA methylation, explaining 39% of its variance. Accurate SINE and LINE transposon methylation in both the mouse and primates can be obtained with just 0.0001× coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology and for low-resource groups.

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“…In carnivores, age clocks were assessed for canids (Ito et al ., 2017; Thompson et al ., 2017, Horvath et al ., 2022 e ), felines (Cantrell et al ., 2020; Raj et al ., 2021; Qi et al ., 2021), mustelids (Lachance et al ., 2015) and pinnipeds (Sareisian, 2014; Robeck et al ., 2023). The first model in the domestic dog, Canis familiaris (Linnaeus) assayed CpGs in six genes and constructed a clock from the four highly age‐correlated CpGs, able to predict age with a MEP of 34–37 months (Ito et al ., 2017).…”

Section: Biological Clocks and Agementioning

confidence: 99%

“…Global methylation has also been studied in pinnipeds in relation to age in the ringed seal [ Phoca hispida (Schreber)], using liver and kidney tissue, however, no clear difference was observed between the sub‐adult and adult groups – possibly due to small sample sizes or tissue type (Sareisian, 2014). Similar studies were performed measuring global methylation using enzyme‐linked immunosorbent assay (ELISA) in bobcats [ Lynx rufus (Schreber)], and fishers [ Pekania pennanti (Erxleben)], using liver samples (Lachance et al ., 2015; Cantrell et al ., 2020). While both identified the same trend of a decrease in methylation with age, supporting the possibility that these species may be well suited to the development of epigenetic clocks for age determination, neither was able to detect a statistically significant difference between young and mature individuals.…”

Section: Biological Clocks and Agementioning

confidence: 99%

Biological clocks as age estimation markers in animals: a systematic review and meta‐analysis

et al. 2023

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Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age‐determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post‐mortem age‐at‐death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less‐invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta‐analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta‐analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age‐estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta‐analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.

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A novel understanding of global DNA methylation in bobcat (Lynx rufus)

Cited by 4 publications

References 31 publications

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates

Biological clocks as age estimation markers in animals: a systematic review and meta‐analysis

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