Measuring Animal Age with DNA Methylation: From Humans to Wild Animals

Paoli-Iseppi, Ricardo De; Deagle, Bruce E.; McMahon, Clive R.; Hindell, Mark A.; Dickinson, Joanne L.; Jarman, Simon

doi:10.3389/fgene.2017.00106

Cited by 76 publications

(95 citation statements)

References 84 publications

(122 reference statements)

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“…Regardless, a targeted gene approach in relation to methylation and exposure of contaminants (e.g. Romano et al 2017) will be necessary to determine the extent to which methylation patterns in our study can reliably indicate age (Paoli‐Iseppi et al 2017).…”

Section: Discussionmentioning

confidence: 99%

Epigenetic response of Louisiana Waterthrush Parkesia motacilla to shale gas development

Frantz

Wood

Latta³

et al. 2020

Ibis

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Epigenetic mechanisms such as DNA methylation may vary in response to environmental stressors and introduce adaptive or maladaptive gene expression within and among wild bird populations. We examined the association between DNA methylation and demographic characteristics of the Louisiana Waterthrush Parkesia motacilla in territories with and without disturbance from shale gas development in a Central Appalachian watershed during 2013–2015. We also evaluated the degree to which an individual’s methylated state was subject to change across years in individuals that returned over the course of more than one breeding season (i.e. recaptures). Overall, population methylation differed between adult male and female Waterthrush where adult males generally had fewer methylated restriction sites. Methylation also differed between adult females and nestlings. Age influenced methylation in both adult males and females with a decrease in methylation with age, although adult female recaptures had increased methylation with age. Adult males were variably methylated between shale gas undisturbed and disturbed areas at a population and restriction site (i.e. loci) level, where restriction sites were predominately less methylated in shale gas‐disturbed areas. Barium (Ba) and strontium (Sr) data from 2013 feather samples showed adult males had fewer methylated sites at higher concentrations of Ba and Sr, whereas nestlings displayed no correlation of methylation to Ba and Sr concentrations. Adult females displayed increased methylation with increased Sr, a trend also seen year to year in adult female recaptures. Overall, results of our study suggest sex‐specific influences of shale gas development on gene expression that may affect long‐term population survival and fitness.

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Section: Discussionmentioning

confidence: 99%

Epigenetic response of Louisiana Waterthrush Parkesia motacilla to shale gas development

Frantz

Wood

Latta³

et al. 2020

Ibis

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“…In both humans and domesticated animals, there is vast literature characterizing genes or genomic regions that either become hyper‐ or hypomethylated with age (Bollati et al., 2009; Christensen et al., 2009; Bell et al., 2012; Gryzinska, Blaszczak, Strachecka, & Jezewska‐Witkowska, 2013; Gryzinska et al., 2016; Spiers et al., 2016). In wild animals, there is growing interest in age‐specific DNA methylation (Paoli‐Iseppi et al., 2017), but few studies have examined this and the results are often contradictory. For example, DNA methylation shows age‐specific linear changes in humpback whales ( Megaptera novaeangliae : Polanowski, Robbins, Chandler, & Jarman, 2014) but no changes in superb starlings (Rubenstein et al., 2016), possibly because these studies selected different candidate genes.…”

Section: Discussionmentioning

confidence: 99%

Age‐ and quality‐dependent DNA methylation correlate with melanin‐based coloration in a wild bird

Soulsbury

Lipponen

Wood

et al. 2018

Ecology and Evolution

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Secondary sexual trait expression can be influenced by fixed individual factors (such as genetic quality) as well as by dynamic factors (such as age and environmentally induced gene expression) that may be associated with variation in condition or quality. In particular, melanin‐based traits are known to relate to condition and there is a well‐characterized genetic pathway underpinning their expression. However, the mechanisms linking variable trait expression to genetic quality remain unclear. One plausible mechanism is that genetic quality could influence trait expression via differential methylation and differential gene expression. We therefore conducted a pilot study examining DNA methylation at a candidate gene (agouti‐related neuropeptide: AgRP) in the black grouse Lyrurus tetrix. We specifically tested whether CpG methylation covaries with age and multilocus heterozygosity (a proxy of genetic quality) and from there whether the expression of a melanin‐based ornament (ultraviolet‐blue chroma) correlates with DNA methylation. Consistent with expectations, we found clear evidence for age‐ and heterozygosity‐specific patterns of DNA methylation, with two CpG sites showing the greatest DNA methylation in highly heterozygous males at their peak age of reproduction. Furthermore, DNA methylation at three CpG sites was significantly positively correlated with ultraviolet‐blue chroma. Ours is the first study to our knowledge to document age‐ and quality‐dependent variation in DNA methylation and to show that dynamic sexual trait expression across the lifespan of an organism is associated with patterns of DNA methylation. Although we cannot demonstrate causality, our work provides empirical support for a mechanism that could potentially link key individual factors to variation in sexual trait expression in a wild vertebrate.

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“…Chromatin and 3D nuclear architecture has been shown to be altered during ageing (Zhang et al, 2015;Sun et al, 2018). At the same time, there is a high correlation of epigenetic marks and ageing in many organism (Horvath, 2013;De Paoli-Iseppi et al, 2017). The progressive loss of epigenetic information, that happen during ageing, could lead to an increased nuclear 3D alteration, and to the consequent alteration of many cellular functions.…”

Section: The "Function" Of Epigeneticsmentioning

confidence: 99%

A non-Lamarckian model for the inheritance of the epigenetically-coded phenotypic characteristics: a new paradigm for Genetics, Genomics and, above all, Ageing studies

Marsellach

2018

Preprint

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In this paper I would like to introduce some theoretical considerations, which, if proven right by the experimental frameworks designed to test them, might stand for a paradigmatic change on genetics, genomics and ageing studies. This paper further develops a theoretical framework previously proposed by this author (Marsellach, 2017). Despite this, this paper is written as a standalone paper, which describe in more detail the previously hinted model (Marsellach, 2017), and adds emphasis in the putative implications that, the proposed theoretical framework, might have in describing the way in which the epigenetic information is transmitted from one generation to the following ones, and in the implications that this might have for genetics, genomics and ageing studies.

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Measuring Animal Age with DNA Methylation: From Humans to Wild Animals

Cited by 76 publications

References 84 publications

Epigenetic response of Louisiana Waterthrush Parkesia motacilla to shale gas development

Epigenetic response of Louisiana Waterthrush Parkesia motacilla to shale gas development

Age‐ and quality‐dependent DNA methylation correlate with melanin‐based coloration in a wild bird

A non-Lamarckian model for the inheritance of the epigenetically-coded phenotypic characteristics: a new paradigm for Genetics, Genomics and, above all, Ageing studies

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