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Метилирование ДНК

Основано на слайдах Jovana Maksimovic и Антонова Ивана

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Talk outline

Epigenetics
DNA methylation
Measuring DNA methylation
Methylation sequencing

What are the challenges?
How does it work?
Suggested analysis pipeline

Summary

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Что такое эпигенетика?

Какие три группы эпегенетических факторов мы выделяли?

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What is epigenetics?

Epigenetics refers to stable heritable traits not explained by changes in DNA sequence

Greek prefix “epi” means “on top of” genetics

Chromosome modifications that affect gene expression

Histones, DNA methylation
“Anything” that isn’t DNA!

Essential for normal development
Can be modified by environment
Can be disrupted in disease

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Epigenetics brings DNA to life!

embryogenesis

blastocyst

zygote

sperm

egg

embryonic stem cells

B cell

T cell

red blood�cell

haematopoietic stem cell

fat�cell

sperm�cell

skin cell

muscle�cell

gland�cell

hormone-�secreting�cell

germ�cell

neuron

astrocyte

neuronal� progenitor

cell

lung�cell

kidney�cell

identical DNA in every cell

different epigenetic patterns

Important in all species

Modified from https://biology.mit.edu/research/stemcell_epigenetics

intestine cell

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Epigenetics is CRAZY complicated!

New sequencing & microarray technologies are enabling us to learn A LOT more about epigenetics

Different data types need different analysis

Today we are only focussing on DNA methylation

Roy et al. (2010), Science

Me

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DNA methylation has a long history of research

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What is DNA methylation?

DNA methylation primarily occurs at CpG dinucleotides

C

G

A

T

C

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DNA methylation in the genome

The human genome contains ~30,000,000 CpGs (~1%)

VERY different between different species

CpGs are not evenly spaced �across the genome

Tend to be present in clusters called CpG islands

CpG methylation is spatially �correlated

Patterson et al. 2011, J Vis Exp

Eckhardt et al. 2007, Nature Genetics

~500bp

Methylation correlation with distance

The human genome contains about 30 million CpGs, which is 1% of the total number of bases in the genome.

But, this varies quite a lot between different species.

A thing to note about CpGs is that they are not evenly spaced across the genome, they tend to be present in clusters that we call CpG islands.

You can see that in this diagram here where the lollipops represent CpGs. You can see that they are sort of randomly far apart and then appear in a tight cluster here.

This represents a CpG island in a promoter, which is quite common as these islands are often colocalised within regulatory regions.

Also of note is that CpGs that are closer together tend to be correlated in their methylation status.

This plot at the bottom shows that methylation within about 500bp is between 60 and 90% correlated but that the correlation is reduced with greater distance.

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Function of DNA methylation: �CpG islands

- (C+G) >= 50%

- Obs CpG / Exp CpG >= 60%

- Length >= 200 bp

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https://www.nature.com/articles/s41467-022-34828-y

genome-wide DNA methylation levels for 500 species, aggregated by taxonomic group

Levels are different between different species

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DNA methylation and evolution

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S-Adenosyl methionine (SAM)

https://www.chem.ucla.edu/~harding/IGOC/S/sam.html

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S-Adenosyl methionine (SAM)

https://www.chem.ucla.edu/~harding/IGOC/S/sam.html

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Methylation can regulate �gene expression

Plot from Peter Hickey

http://meeting.dxy.cn/oemethylation2012/article/i18782.html

Methylation at a single CpG vs. gene expression

Each point is one sample

Methylation is important because it can regulate the expression of genes.

So, sometimes we see a relationship between methylation and gene expression that looks like what you see here in this plot on the right.

Each point in this plot is from one sample and DNA methylation is shown on the x axis and gene expression is on the y

And you can see that as DNA methylation increases gene expression decreases and vice versa.

Now the reason that this can happen is shown here on the left.

You can see that in a normal cell, the CpG lollipops in the body of the gene are methylated, while the ones in the promoter are unmethylated and so this gene is expressed in a normal cell.

However, in cancer for example, we can lose the methylation in the gene body and gain methylation in the promoter, which can lead to this gene being supressed.

This is when you see the sort of relationship show in this plot.

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DNA methylation and cancer

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Methylation changes coat colour of Agouti mice

Dolinoy 2008, Nutr Rev.

This gene controls coat colour in Agouti mice

These CpG sites in the promoter change PS1A expression depending on methylation

These mice are genetically identical

Hypomethylated

Hypermethylated

Coat colour different due to different maternal diet i.e. environment!

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Methylation makes worker bees!

Cridge et al. 2015, Nutrients

These larvae are genetically identical

Hypomethylated

Hypermethylated

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https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00522-4/fulltext

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Enriched pathways for implicated genes from current smoking, recent quitting, in utero smoking exposure, and environmental tobacco smoke exposure models

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TET proteins demethylate cytosines

https://doi.org/10.1038/nrg.2017.33

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Sensitivity of transcription factors to DNA methylation

https://doi.org/10.1042/EBC20190033

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Summary

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Methyl-seq pipeline

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Additional literature