Heritability of DNA methylation in threespine stickleback (<i>Gasterosteus aculeatus</i>)

Hu, Juntao; Wuitchik, Sara J S; Barry, Tegan N.; Jamniczky, Heather A.; Rogers, Sean M.; Barrett, Rowan D. H.

doi:10.1093/genetics/iyab001

Cited by 36 publications

(54 citation statements)

References 141 publications

(199 reference statements)

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“…DNA methylation) as well as heritable genetic and epigenetic changes across generations (e.g. single nucleotide polymorphisms, maternal effects) [70,71]. To examine epigenetic effects, DNA methylation patterns (for example) in genetically similar individuals that also show divergence in physiological traits could be compared.…”

Section: Evidence For Local Adaptationmentioning

confidence: 99%

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Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating

et al. 2021

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To better understand temperature's role in the interaction between local evolutionary adaptation and physiological plasticity, we investigated acclimation effects on metabolic performance and thermal tolerance among natural Fundulus heteroclitus (small estuarine fish) populations from different thermal environments. Fundulus heteroclitus populations experience large daily and seasonal temperature variations, as well as local mean temperature differences across their large geographical cline. In this study, we use three populations: one locally heated (32°C) by thermal effluence (TE) from the Oyster Creek Nuclear Generating Station, NJ, and two nearby reference populations that do not experience local heating (28°C). After acclimation to 12 or 28°C, we quantified whole-animal metabolic (WAM) rate, critical thermal maximum (CT max ) and substrate-specific cardiac metabolic rate (CaM, substrates: glucose, fatty acids, lactate plus ketones plus ethanol, and endogenous (i.e. no added substrates)) in approximately 160 individuals from these three populations. Populations showed few significant differences due to large interindividual variation within populations. In general, for WAM and CT max , the interindividual variation in acclimation response (log 2 ratio 28/12°C) was a function of performance at 12°C and order of acclimation (12–28°C versus 28–12°C). CT max and WAM were greater at 28°C than 12°C, although WAM had a small change (2.32-fold) compared with the expectation for a 16°C increase in temperature (expect 3- to 4.4-fold). By contrast, for CaM, the rates when acclimatized and assayed at 12 or 28°C were nearly identical. The small differences in CaM between 12 and 28°C temperature were partially explained by cardiac remodeling where individuals acclimatized to 12°C had larger hearts than individuals acclimatized to 28°C. Correlation among physiological traits was dependent on acclimation temperature. For example, WAM was negatively correlated with CT max at 12°C but positively correlated at 28°C. Additionally, glucose substrate supported higher CaM than fatty acid, and fatty acid supported higher CaM than lactate, ketones and alcohol (LKA) or endogenous. However, these responses were highly variable with some individuals using much more FA than glucose. These findings suggest interindividual variation in physiological responses to temperature acclimation and indicate that additional research investigating interindividual may be relevant for global climate change responses in many species.

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Section: Evidence For Local Adaptationmentioning

confidence: 99%

“…DNA methylation data in combination with genetic data could also be used to identify single nucleotide polymorphisms important for explaining variation in methylation patterns important for physiological trait variation (i.e. meQLT analysis [71]).…”

Section: Evidence For Local Adaptationmentioning

confidence: 99%

Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating

et al. 2021

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“…Due to mental, physical, and sexual abuse suffered at the age of 3-5, DNA methylation occurs in a specific region, and the methylation pattern is preserved even after adulthood; also, environmental factors affect such individuals [15]. Environmental factors, recorded in the form of population DNA methylation patterns, are preserved across generations [12]. In that study, unknown genomic changes may have been involved in DNA methylation patterns at specific sites, and the simple concept of "epigenetics = inheritance of acquired traits" is a trait in genetics.…”

Section: Prospects For Epigenetics and Methylated Cytosinementioning

confidence: 99%

Histochemistry, Cytochemistry and Epigenetics

Kitazawa

Ohno

Haraguchi

et al. 2022

Acta Histochem. Cytochem

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Over the past few decades, many researchers have individually identified tumor-related genes, and have accumulated information on their basic research in a database. With the development of technology that can comprehensively test the expression status within a short time, oncogene panel testing has become attainable. On the other hand, changes in gene expression that do not depend on changes in base sequences, that is, epigenetics, or more comprehensively, epigenomes, are also highly involved in the development and progression of disease. Oncogene panel tests tend to focus on DNA base mutations such as point mutations, deletions, duplications, and chimera formation. Elucidation leads to correct interpretation of diseases and treatment choices, and we are in an era where integrated understanding of the genome and epigenome is indispensable. In this review, we make every effort to cover a wide range of knowledge, including data on histone protein modification, non-coding (nc)RNA and DNA methylation, and recent application trials for demonstrating epigenetic alterations in histologic and cytologic specimens. We hope this review will help marshal the knowledge accumulated by researchers involved in genomic and epigenomic studies.

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“…For example, in sticklebacks, some but not all population-level variation in DNA-Me is correlated with plasticity-induced by differences in water salinity (Heckwolf et al, 2020). Some of these methylation changes have been linked to cis or trans-acting loci which show evidence of local adaptation (Hu et al, 2021). Similarly, population level changes in gene body methylation that appear in corals inhabiting different quality environments are associated with higher genetic differentiation at those loci (Dixon et al, 2018).…”

Section: Sources Of Variation In Dna Methylationmentioning

confidence: 99%

“…However, there are a number of pathways through which epigenetic marks could participate in adaptative processes and contribute to the emergence of population-level changes. For example, epigenetic marks could be a byproduct of transcriptional states or genetic sequence change (Dixon et al, 2018;Dubin et al, 2015;Hu et al, 2021). In this scenario epigenetic modifications are effectors and/or markers rather than drivers of the adaptive change.…”

Section: Introductionmentioning

confidence: 99%

Evolved changes in DNA methylation in response to the sustained loss of parental care in the burying beetle

Mashoodh

Sarkies

Westoby

et al. 2021

Preprint

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Levels of parental care critically influence the development environment with the capacity to impact the growth, survival, physiology, and behaviour of offspring. Plastic changes in DNA methylation have been hypothesised to modulate gene expression responses to parental environments. Moreover, these effects can be inherited and so may affect the process of adaptive evolution. In this study, using experimental evolution, we investigated how plastic changes in DNA methylation induced by the loss of parental care have evolved in a biparental insect (Nicrophorus vespilloides) using experimental evolution. We show that removal of care in a single generation is associated with changes in gene expression in stress-related pathways in 1st instar larvae. However, in larvae that have adapted to the loss of parental care after being deprived of care for 30 generations, gene expression is shifted from stress-related gene expression towards growth and brain development pathways. We found that changes in gene body methylation arose both as a direct response to the loss of parental care and stochastically as populations diverged. Overall, our results suggest that a complex interplay between transcription and DNA methylation shapes the molecular adaptation to environmental change.

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Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus)

Cited by 36 publications

References 141 publications

Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating

Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating

Histochemistry, Cytochemistry and Epigenetics

Evolved changes in DNA methylation in response to the sustained loss of parental care in the burying beetle

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