Introduction to Epigenetics Implications for Human Nutrition Outline

• Epigenetics in Action

• Defining (Epi)genetics

• ‘Writers’, ‘Readers’ and ‘Erasers’ of epigenetic information

• Environmental Epigenomics Nutri(Epi)genomics

Epigenetics: “what makes us different even when we are equal”

Agouti viable Rainbow yellow

Carbon-copy Epigenetics: “what makes us different even when we are equal”

- hundreds of different kinds of cells in our bodies

- each one derives from the same starting point and has the same 20000 odd genes

- as cells develop, their fate is governed by the selective use and silencing of genes

- this process is subject to epigenetic factors

http://www.ncbi.nlm.nih.gov/About/primer/genetics_cell.html (Epi)genetics

• The study of:

‘Any heritable alteration in gene function that does not result in a change in DNA sequence but will have a significant impact on the development of the organism’

The epigenetic marks

• DNA Methylation (Me) • Histone modifications (mod) • Non-coding RNAs (ncRNA)

www.Epigenome-noe.net/

Epigenetics deals with modifications of chromatin (DNA and associated proteins) which are heritable, reversible and affect genome function (transcription, replication, recombination, chromosome structure, etc.) Why is Epigenetics important?

Epigenetics creates a memory of cell identity

www.Epigenome-noe.net/ AHEAD Epigenome project (2008) Nature 454: 711 Why is it important to maintain cellular memory? Differentiated cell (e.g.liver cell) + liver cell + liver cell

CH3 CH3 CH3

Ac Ac Ac

CH3 CH3 CH3

Ac Ac Ac

CH3 CH3 CH3

“Fixed epigenotype” Dedifferentiated cell Cancer Ac Loss of memory Rett Syndrome (“variegating” Ac ICF Syndrome CH3 Fragile X epigenotype) CH3 BWS Ac Prader-Willi Epigenetics and Gene Transcription

Transcription complex Accessible / Active Nucleosome

Active histone modification

Repressive histone modification OFF DNA methylation

Transcription No transcription Condensed / Silent The 5th Base of DNA: Cytosine DNA methylation

Dnmts (1, 3a, 3b, 3L) Methyl binding proteins DNA methylation machinery Passive demethylation (writers, readers & erasers) Active demethylation: - Enzymes? - via DNA repair?

Epigenetic phenomena associated with DNA methylation

Bulk genomic DNA is subject to low density CpG island methylation

mCG CG

• Genomic stability and control of transposon activity • Genomic imprinting in plants and mammals • X-inactivation in mammals • Transcriptional regulation (cell differentiation; cancer biology) How is methylated DNA translated into a silencing signal?

1. Repulsion of transcription factors

2. Attraction of Repressors/repulsion of activators

Sasai & Defossez (2009) Int J Dev Biol 53:323; Bogdanovic & Veenstra (2009) Chromosoma 118:549 Histones are subject to hundreds of modifications

Histone modifications serve to recruit and bind critical DNA-regulatory proteins that control transcription, replication, recombination and repair – an HISTONE CODE? Complex histone modification machinery (writers, readers and erasers) In In Epigenetics (eds. Allis, Jenuwein, Reinberg), CSH Press, 2007 Histone Acetylation

In Epigenetics (eds. Allis, Jenuwein, Reinberg), CSH Press, 2007 Histone methylation

H3K27 methylation H3K4 methylation (repressive OFF) (activating ON)

In Epigenetics (eds. Allis, Jenuwein, Reinberg), CSH Press, 2007 Pharmaco(epi)genomics

In Epigenetics (eds. Allis, Jenuwein, Reinberg), CSH Press, 2007 Non-coding RNAs

 Long non-coding RNAs (> 2Kb long)

 Short non-coding RNAs (siRNAs, miRNAs, PiwiRNAs, snoRNAs) (21nt to 300 nt)

Many Involved in silencing pathways: through chromatin-dependent gene silencing pathways (e.g. lncRNAs) or RNA degradation or translation arrest (e.g. miRNAs) Disruption of ncRNAs linked to human disease:

The imprinted Kcnq1ot1 lncRNA How dynamic is the Epigenome?

• Epigenetic marks are stably propagated during cell division and contribute to cell lineage determination • But they can switch from being “stable” to being “flexible”:

Reprogramming of the epigenetic information during development (somatic epigenetic patterns need to be ‘reset’ or ‘reprogrammed in germ cells and also in early embryos in order to achieve developmental pluripotency)

Jirtle RL and Skinner MK (2007) Nat Rev Genet 8:253-262

How dynamic is the Epigenome?

Epigenetic states can undergo regulated change in response to particular stimuli in order to modulate gene expression as the need arises (e.g. response to external environmental factors)

Genome

how the genome integrates intrinsic and environmental signals Epigenetics Environment Environmental Epigenomics

• Evidence that links epigenetics as potential mechanistic explanation for the long- term impact of the environment on physiology and behavior:

Royal Jelly – the ultimate Vernalization in Epigenetic studies in diet evolution plants in Monozygous twins

3year-old 50 year-old Nutritional control of Epigenetic responses to reproductive status in cold temperatures & Divergent Disease honeybees via DNA long-term memory susceptibility? methylation

Environmental Epigenomics II

“A mother’s behaviour can Endocrine disruptors and affect the chemistry of DNA in transgenerational effects her offspring…” of environmental insults

Maternal care controls level of DNA methylation Decrease in spermatogenesis not only of the glucocorticoid receptor in the in treated animals but in males of Hypocampus of offspring, with long- several subsequent generations (F1- term effects F4)- Altered DNA methylation?

Effect of diet on DNA methylation and phenotype in offspring

Maternal Nutrition in Avy mice:

Jirtle RL and Skinner MK (2007) Nat Rev Genet 8:253-262 Maternal diet and offspring health

Suboptimal diet

Gene expression changes in fetus

Cellular memory of suboptimal early nutrition Aging Effects on tissue function

Metabolic Disease HNF4a – Master Regulator

Pancreatic tissue development Pancreatic tissue function (fetal life) (adult life) Nutritional programming model Dietary effects on Epigenetic Regulation of Enhancer-Promoter Interactions YOUNG ADULTS OLD ADULTS Normal diet

Enh P2 Enh P2 +++ ++ Activating Enhancer P Promoter Silencing Low protein diet

P2 Enh P2 Enh ++ Enhancer-specific + epigenetic modifications

Ozanne S et al. (2011) Aging 5:548 Sandovici I et al. (2011) Proc Natl Acad Sci 108:5449 Conclusions

• Maternal diet and age reduces Hnf4a expression

• The mechanism of this reduction is epigenetic

• Maternal diet exacerbates the epigenetic silencing during aging

• These changes explain why poor diet during pregnancy leads to increased risk of diabetes in the offspring

• Similar mechanisms operate in human islets Nutri(Epi)genomics

• There is now clear evidence that dietary factors influence epigenetic marking of genes, both in animal and human population studies (e.g. folic acid, methyl donors, choline, selenium, genistein, protein, butyrate, etc.)

• However little is known about precise mechanisms, doses of dietary factors and duration of exposure/depletion needed to provoked changes and the extent of which these are tissue-specific

• Likely that epigenetic changes will occur by (i) altering abundance or efficacy of the “writers” and “erasers” of epigenetic information, and/or by (ii) altering the availibility of substrates Points for discussion

- epigenetic factors govern the interpretation of DNA within each living cell

- understanding these factors will revolutionize evolutionary and developmental biology, and thus affect practices from medicine to agriculture

- hereditary, environmental and stochastic factors determine the accumulation of epigenetic variation over time – their relative contribution to phenotypic variation and increased risk of common diseases remains largely unknown

- epigenetics is a potential mechanistic explanation for the long-term impact of the environment on physiology and behavior (e.g acting on windows of epigenetic “reprogramming”)

- potential applications in clinical practice:

epigenetic biomarkers for early diagnosis of disease preventive measures based on diet drugs that target epigenetic marking of specific genes