Methylomes: Overview, potential for plasticity andfor short-term adaptation

Alexander Jueterbock

2016-10-19

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What is the methylome?

The set of DNA methylation modifications in an organism’s genome

(Zakhari, 2013)

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DNA methylation often represses gene expression

DNA methylation represses transcription when it occurs in

promoter regions (DNA region initiating gene expression)

transposable elements (jumping genes)

source: http://cnx.org/contents/QcTHfqRM@1/Basic-Principles-of-Genetics

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DNA methylation adds a level of variation to the genome

(Allis et al., 2015)

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DNA-methylation heritability and adaptive potential

http://www.atdbio.com/content/56/Epigenetics

Resetting during gameto- and embryogenesis

Maintenance during mitosis

Spontaneous epimutations

6.37x104 faster than genetic mutation rate (Schmitz et al.,2011)

Response to environment

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Resetting versus memory in DNA methylation response

(Crisp et al., 2016)

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Example of heritable, environmentally induced adaptation

Artificial offspringdemethylation withzebularine removes adaptiveeffect of parental drought inPolygonium persicaria

(Herman et al., 2016)

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Eco-evolutionary importance of DNA-methylation

SpeciationHeritable phenotypic variationAdaptation independant ofgenotype

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Adaptive potential of DNA methylation higher in plantsthan in animals

Late separation of germline from somatic tissue, offspringmethylome affected by parents’ environment

Methylome less erased during gameto- and embryogenesis

Epigenetic reprogramming not restricted to gameto- andembryogenesis

(Sessile nature requires rapid response to the environment)

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Compensation for absence of genetic variation

Methylation variation of genetically identical individuals increased

productivity (biomass by 40%)

stability (pathogen and competitor resistance)

(Latzel et al., 2013) Arabidopsis thaliana

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What is known in seagrass

DNA (cytosine-5-)-methyltransferase present in the genome

DNA cytosine methylation confirmed in our lab

Clonality is ideal to study adaptive value of methylation

Genetic variation is not a confounding factor

Epigenetic variation may be more relevant than for sexualreproducing organisms (Douhovnikoff and Dodd, 2014)

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Questions - where to go?

De Novo methylome in seagrass

Methylation variation

between clones within a meadow

geographic variation (range edges vs centers)

associated with environmental differences

importance in clonal vs non-clonal meadows

increase of stress resilience in the absence of genetic variation?

Methylation response

autonomous methylation changes (decoupled from geneticchanges) in response to different stress factors

effect on the activity of transposable elements

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References I

Allis, CD, ML Caparros, T Jenuwein, and D Reinberg (2015).Epigenetics. P. 984.

Crisp, PA, D Ganguly, SR Eichten, JO Borevitz, and BJ Pogson(2016). “Reconsidering plant memory: Intersections betweenstress recovery, RNA turnover, and epigenetics”. In: ScienceAdvances 2.2, e1501340–e1501340.

Douhovnikoff, V and RS Dodd (2014). “Epigenetics: a potentialmechanism for clonal plant success”. In: Plant Ecology 216.2,pp. 227–233.

Fieldes, MA and LM Amyot (1999). “Epigenetic control of earlyflowering in flax lines induced by 5- azacytidine applied togerminating seed”. In: Journal of Heredity 90.1, pp. 199–206.

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References II

Herman, JJ, SE Sultan, and JJ Herman (2016). “DNA methylationmediates genetic variation for adaptive transgenerationalplasticity”. In: Proceedings of the Royal Society of London B:Biological Sciences 283.1838.

Latzel, V, E Allan, A Bortolini Silveira, V Colot, M Fischer, andO Bossdorf (2013). “Epigenetic diversity increases theproductivity and stability of plant populations.” In: Naturecommunications 4, p. 2875.

Schmitz, RJ, MD Schultz, MG Lewsey, RC O’Malley, MA Urich,O Libiger, et al. (2011). “Transgenerational epigenetic instabilityis a source of novel methylation variants.” In: Science (NewYork, N.Y.) 334.6054, pp. 369–373.

Zakhari, S (2013). “Alcohol metabolism and epigenetics changes”.In: Alcohol Res.

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