ANHB3323 epigenetics

What is epigenetics?

Study of heritable change si gene expression that occur without directly altering the underlying DNA sequence.

• DNA is wrapped around histones

• nucleosomes are strung together

• comprises chromatin fibre

• how packed chromatin in affects how it is read

• epigenetics are ADDED or REMOVED mods for how genes are read (reversible)

Explain gene expression and chromatin¤

Epigenetic processes

Main two:

DNA methylation

Histon emodification

Also non-coding RNAs (ncRNAs) - anything that controls chromatin structure

Chemical modificaiton to DNA - DNA methylation

DNA methylation

• heritable mark

• covalent transfer of methylg group to cytosine ring

• typically at CpG dinucleotine (cytosine-phosphate-guanine)

• in the context of promoter region - increased methylation —> gene repression

• DNA methyltransferased DNMT3A and DNMT3B establish methylation patterns in combination with DNMT3L

• DNMT1: maintainence methyltransferase

• these enzymes control addition or removal

Chemical modifications - histone modification

• post-translational mod of histone proteins

• methylation, phosphorylation, acetylation, ubiquitylation and sumoylation

• impact chromatin structure

• affect histone-DNA or histone-histone interacrions

• recruit histone modifiers

• histone modificaiton occuring can recruit more modifiers

Histone acetylation

• tails produce off of histone proteins

• writers of acetylation - histone acetyltransferases enzymatically add acetyl group

• erasers- histone deacetylases remove acetyl group

• acetylation = active gene regions

• deacetylaiton = repressed

histone methylation

• more stable than acetylation

• occurs on lysine and arginie residues on histone tales

• more complex: mono-, di-, tri-meethyl

• generally associated with gene reprsioon - sometimes activation

• histone demethylases - add group

• histone methyltransferase - remove group

Non-coding RNA

• RNA that do not have role in coding protein

• long nCRNAs = >200 nucleotides and up to 100 kilobases

• short ncRNAs = <200 (microRNAs most studied in cancer)

• microRNA small single stranded: 18-22bp length

• can drive sequence for degradation

• sponging miRNA can prevent lncRNA from modifying

• lncRNA can act as decoy to bind to marker instead of the marker binding to DNA

Cancer

• epigenetic and genetic alterations affect phenotypic plasticity

• cancer cell heterogeneity —> spectrum of cellular behaviours

• ^contributed heavily to resistance

• epigenetic landscape altered in cancer - involcing epigenetic alterations to DNAmethylaiton and histone modification

• spectrum of cell s(Eg. ‘“ïnbetween cells”’ not mesenchymal and not epithelial)

Role of epigenetics in cancer

• organisation of chromatin structure differs between cell types

• in cancer cells the organisation is similar to stem cells or reprogrammed cells

• tumour supressor genes are repressed - inactive, mutated or silaced or deleted relative to normal tissue

• oncogneic genes - overexpressed or overactive: maintain uncontrolle dporliferation, active migrationa nd invasion, promote drug resistance

Abnormal epigenetics in cancer

• tumour cells have different “methylome”compared to normal cells

• demethylation of promoter region sof oncogenes

• OR increased in focal methylaiton also obsrved - methylation at promoter region of tumour supressor cells

Epithelial to mesenchymal transition

• In normal conditions there is increased pro-epithlial miRNAs which keep mesenchynal trancription factors in check

• upregulation of pro-epithelial markers —> give rise to non-motile peithelial cells tjat have good cell-cell adhesion an dpolarity

• In cancer miRNA silenced by epigenetic markers —> transcription factors activated

• lose cell-cell adhesion and polarity and become elongated so they can migrated

• cells become more resistant to drugs

Epigenetics feedback loop

• e-cadherin gives structure to membrane of epithelial cells - maintain phenotype

• tramscription factors bind to e-boxes in front of epithelial genes —-
  > can recruit epigenetic modifiers to promoter region of genes

• can remodel chromatin, add histone marks, add methylation or remove

• can silence E-cadherin (CDH1 encodes for it)

• loss of e-cad enabled tumour cells to metastisise

• n-cadherin increased when e-cadherin decreased - CDH2 increases

• miRNA can repress transcript of ZEB1

example: histone marks on oncogenic ZEB1 promoter

• in non-cancer state ZEB1 is repressed by K27Me3

• In cancer stem cell like state it has activaito mark of K4ME3

• in hybrid state the ZEB1 promoter had both marks

• bivalent mark - both on promoter

• ZEB1 can switch on or off in response to environmental stimuli

epigenome editing

• manipulate epigenome

• 3 molecular platforms developed- zinc finger proteins

  • simple to engineer and deliver

  • small - wide variety of context/use

  • lots of off target effects

• transcription activator-like effectors

• CRISPR and CRISPR-Cas