Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects
Sepers B, Chen R, Memelink M, Verhoeven KJF, van Oers K (2023)
Molecular Biology and Evolution 40(4).
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| Veröffentlicht | Englisch
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**Abstract**
As environmental fluctuations are becoming more common, organisms need to rapidly adapt to anthropogenic, climatic, and ecological changes. Epigenetic modifications and DNA methylation in particular provide organisms with a mechanism to shape their phenotypic responses during development. Studies suggest that environmentally induced DNA methylation might allow for adaptive phenotypic plasticity that could last throughout an organism's lifetime. Despite a number of studies demonstrating environmentally induced DNA methylation changes, we know relatively little about what proportion of the epigenome is affected by environmental factors, rather than being a consequence of genetic variation. In the current study, we use a partial cross-foster design in a natural great tit (Parus major) population to disentangle the effects of common origin from common rearing environment on DNA methylation. We found that variance in DNA methylation in 8,315 CpG sites was explained by a common origin and only in 101 by a common rearing environment. Subsequently, we mapped quantitative trait loci for the brood of origin CpG sites and detected 754 cis and 4,202 trans methylation quantitative trait loci, involving 24% of the CpG sites. Our results indicate that the scope for environmentally induced methylation marks independent of the genotype is limited and that the majority of variation in DNA methylation early in life is determined by genetic factors instead. These findings suggest that there may be little opportunity for selection to act on variation in DNA methylation. This implies that most DNA methylation variation likely does not evolve independently of genomic changes.
As environmental fluctuations are becoming more common, organisms need to rapidly adapt to anthropogenic, climatic, and ecological changes. Epigenetic modifications and DNA methylation in particular provide organisms with a mechanism to shape their phenotypic responses during development. Studies suggest that environmentally induced DNA methylation might allow for adaptive phenotypic plasticity that could last throughout an organism's lifetime. Despite a number of studies demonstrating environmentally induced DNA methylation changes, we know relatively little about what proportion of the epigenome is affected by environmental factors, rather than being a consequence of genetic variation. In the current study, we use a partial cross-foster design in a natural great tit (Parus major) population to disentangle the effects of common origin from common rearing environment on DNA methylation. We found that variance in DNA methylation in 8,315 CpG sites was explained by a common origin and only in 101 by a common rearing environment. Subsequently, we mapped quantitative trait loci for the brood of origin CpG sites and detected 754 cis and 4,202 trans methylation quantitative trait loci, involving 24% of the CpG sites. Our results indicate that the scope for environmentally induced methylation marks independent of the genotype is limited and that the majority of variation in DNA methylation early in life is determined by genetic factors instead. These findings suggest that there may be little opportunity for selection to act on variation in DNA methylation. This implies that most DNA methylation variation likely does not evolve independently of genomic changes.
Stichworte
epigenetics;
DNA methylation;
vertebrate;
mQTL;
cross-fostering
Erscheinungsjahr
2023
Zeitschriftentitel
Molecular Biology and Evolution
Band
40
Ausgabe
4
Urheberrecht / Lizenzen
ISSN
0737-4038
eISSN
1537-1719
Page URI
https://pub.uni-bielefeld.de/record/2988694
Zitieren
Sepers B, Chen R, Memelink M, Verhoeven KJF, van Oers K. Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects. Molecular Biology and Evolution. 2023;40(4).
Sepers, B., Chen, R., Memelink, M., Verhoeven, K. J. F., & van Oers, K. (2023). Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects. Molecular Biology and Evolution, 40(4). https://doi.org/10.1093/molbev/msad086
Sepers, Bernice, Chen, Rebecca, Memelink, Michelle, Verhoeven, Koen J F, and van Oers, Kees. 2023. “Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects”. Molecular Biology and Evolution 40 (4).
Sepers, B., Chen, R., Memelink, M., Verhoeven, K. J. F., and van Oers, K. (2023). Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects. Molecular Biology and Evolution 40.
Sepers, B., et al., 2023. Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects. Molecular Biology and Evolution, 40(4).
B. Sepers, et al., “Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects”, Molecular Biology and Evolution, vol. 40, 2023.
Sepers, B., Chen, R., Memelink, M., Verhoeven, K.J.F., van Oers, K.: Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects. Molecular Biology and Evolution. 40, (2023).
Sepers, Bernice, Chen, Rebecca, Memelink, Michelle, Verhoeven, Koen J F, and van Oers, Kees. “Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects”. Molecular Biology and Evolution 40.4 (2023).
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