Epigenetics Flashcards
What is epigenetic?
Heritable changes (between cell lines, not generations) that are not caused by changes in DNA sequence
What are the normal functions of epigenetics?
Cell differentiation
X chromosome inactivation
Embryonic development
Gene imprinting
What are the two epigenetic modifications?
DNA methylation
Histone Modification
How does DNA methylation work?
Addition of a methyl group on to the 5 position of a cytosine in a CpG site - forms 5-MC
Catalysed by DNMT1/3a/3b
DNMT 1 - inheritance - affinity for semi methylated DNA
DNMT 3a/3b - de novo - equal affinity for hemi and non methylated DNA - supported by DNMT 3L
Doesn’t occur in CpG islands - errors can lead to CANCER
How does DNA methylation affect gene expression?
1) Methylation of CpG sites in TF affect binding to the DNA (not all TFs have CpG sites)
2) Methylation of DNA causes recruitment of 2 methyl binding protein complexes - MBD2 and MeCP2 - contain HDACs which inactivate DNA (conversion to heterochromatin)
What other sites can DNA methylation occur at?
CpA, CpT (embryonic stem cells), CpC
What are the different forms of histone modification?
Acetylation - Lysine - HAT/HDAC - affect charge - use Acetyl CoA as cofactor
Methylation - Lysine - HKMT with SAM (cofactor) - K27/K9 (H3) inactive - K4 (H3) - active - Arginine - RME Type 1 and Type 2 - use SAM as cofactor
Phosphorylation - Serine/Threonine/Tyrosine - Kinase/phosphotase - transfer ATP to OH group of AA - introduce negative charge which affects binding of chromatin
What is epigenetic drift?
With age, our epigenetic change:
- Increase in methylation within CpG islands
- Reduction of methylation in global genome
- Increase in mutations within CpG sites (5-MC more prone to mutation)
How can DNA methylation be linked to cancer?
High methylation within promoter sequences of Tumour suppressor genes (CpG islands) leads to suppression of expression
Reduced global methylation - reduced genome stability - cell transformation
Increased mutations within CpG sites
What techniques have we used to identify DNA methylation links with cancer?
Bisulfite modification - allows for study of methylation across multiple genes - indentified CIMP (CpG Island methyl Phenotypes) and Type A/C genes
What drug can we use to target DNA methylation with the aim of treating cancer?
Azacitidine - DNA methyltransferase inhibitor - Myelodysplastic syndrome
What are the two classes of HDAC?
Zn dependent - Class 1,2,4
NAD dependent - SIRTS
What is an example of an HDACi?
Zolinza - Cutaenous T Cell Lymphoma - targets active site of HDAC and chelates Zn ions - targets Class 1, 2, 4
What environmental effects can influence epigenetic?
Diet (Folate, HFHS, med diet)
Smoking
Endocrine disruptors (Bisphenol A, vinclozinin, phthalates)
Behaviour (PA, maternal grooming, early life trauma)
How can diet influence epigenetics?
Folate - SAM - retro transposal element - agouti mice experiment
HFHS diet - autonomic NS impact (CVD) - reduction in ACE methylation - increase in ACE 2 gene expression - increase in autonomic NS dysfunction - CVD
Med diet - study giving mothers omega tablets - using bisulphite sequencing found that children had increased IGF2 hypermethylation - IGF2 increase in seen in diabetic patients
How can smoking influence epigenetics?
Smoking can affect epigenetics in both adult life (over 2500 CpG sites - CVD, obesity etc) and during pregnancy (over 500 CpG sites) - can lead to problems such as LBW, SIDS and addiction later in life
Thought to cause effect from cigarette smoke - damages DNA (double strand breaks) - leads to altered DNA methylation patterns. Also thought to impact on DMT1 - affecting inheritance of methylation patterns. Also increase in smoking smoke increases hypoxia and this leads to recruitment of more SAM (cofactor for DNA methylation) so results in increased methylation
How can endocrine disruptors influence epigenetics?
Bisphenol A (plastic manufacture) - exposure during sensitive periods (in uterus, infancy, adolescence) can lead to cancer, obesity though impact on DNA methylation
Phthalates - plastic manufacture - 300 children cohort study looking at parental exposure to this before pregnancy and risk of hypospadias - found that paternal occupation influenced risk of hypospadias, with those exposed to high Phthalates having higher hypospadias risk.
Vinclozinin (fungicides) - shows heritability of epigenetic changes - pregnant mice - passed on to foetus and germline cells - affects sperm motility
What are the classes of HDAC?
18 in human - HDAC 1-11 (Zn dependent - Class 1, 2, 4) - SIRT (1-7 - NAD dependent)
What studies have shown an associated between ageing/chronic disease and HDAC?
C.elegens - increase of SIR2 (homologue of SIRT1) increased lifespan
Drosophila - resveratrol (increases activity of SIRT2) increases lifespan
Drosophila - caloric restriction (increases SIRT2) increases lifespan
Mice - caloric restriction associated with health benefits (heart disease, obesity, liver disease, mood, brain injury recovery, diabetes)
Mice - caloric restriction alleviated symptoms of machado-joseph syndrome (CNS disease with muscular degeneration and loss of control)
What is the impact if we give someone a HDACi for treatment of cancer (such as Zolinza)?
Reduces cancer - increased ageing - reduced lifespan - alleviates other chronic diseases such as liver disease, heart disease and diabetes.
