lecture 30 Flashcards
1
Q
Objectives and outline
A
- to understand the principles of DNA metabolism in the context of chromatin – epigenetic mechanisms
- introduction – DNA as the “lifeless” blueprint
→ identical twin studies
→ lessons from differential feeding in early development: diet and epigenetics
→ DNA packaging and DNA metabolism
→ DNA damage and repair – histone variants - DNA methylation in health and diseases
→ aberrant DNA methylation in cancer
→ DNMT inhibitors - emerging cancer therapies - histone post-translational modifications
→ histone methylation
→ histone acetylation
→ histone deactylase inhibitors - emerging cancer therapies
2
Q
What is epigenetics?
A
- still controversial and we will develop an accepted definition throughout the lecture
- literal definition
- “genetics” = greek derived from “genesis” – birth, origin
“epi” = greek for “above, beyond) - derived from the virtually redundant Aristotelian word of epigenesis, which was used by the Hellenic philosopher to describe his theory of gradual and progressive developmental changes
- the term epigenetics was introduced by the British scientist Conrad Waddington in the 1940s to incorporate all of the factors controlling gene expression and cell differentiation
- proposed the concept of an epigenetic landscape to represent the process of cellular decision-making during development
- at various points in this dynamic visual metaphor, the cell (represented by a ball) can take specific permitted trajectories, leading to different outcomes or cell fates
“Heritable changes in gene expression and cellular phenotype that are independent of changes in the underlying DNA sequence)
3
Q
Who are some current authorities on epigenetics?
A
- professor adrian bird: university of edinburgh (DNA methylation; Rett syndrome
- professor tony kouzarides - the gurdon institute, cambridge (histone post-translational modifcations)
- professer john mattick – university of queensland (RNA regulation)
4
Q
What is the human genome?
A
- DNA double helix is “lifeless” - contains the blueprint but requires instructions!
- the human genome contains approximately 20,000-25,000 genes
- genes encode proteins that perform most life functions
- only 1-2% of the human genome is made up of genes
- the function of many genes and the vast remainder of sequences in the human genome are yet to be fully understood
5
Q
What is non-coding RNA?
A
- originally referred to as “junk” DNA
- regulatory sequences – critical biochemical functions
- encyclopedia of DNA elements (ENCODE)
6
Q
What is link between genetics and disease?
A
- many diseases have a well known genetic basis
- e.g. BRCA1/BRCA2 mutations in breast/ovarian cancer
7
Q
What is an example of twins and disease?
A
breast cancer
- when loretta was diagnosed with breast cancer, lorraine was in the doctor’s office with her
- loretta asked if lorraine should be checked as well
- the doctor discovered that lorraine aslso had breast cancer
- after receiving treatment, the sisters are both in good health
8
Q
What is epigenetic drift?
A
- identical twins are born with the same epigenome
- epigenetic profiles begin to diverge as they age
- differences increase as twins live longer and spend more time apart
1. epigenetic marks are removed randomly as people age
2. environmental influences change the pattern of epigenetic marks
epi-twin study
intra-specific variations in healthspan and lifespan:
- nature, nurture, chance
- chance dominations
9
Q
What is an example of differential feeding?
A
apis mellifera
- caste switching
- based solely on differential feeding during development (royal jelly)
- royalactin – growth factor receptors (kamakura, royalactin induces queen differentiation in honeybees)
- chromatin modifications – histone deacetylase inhibitor ? (Spannhoff et al. Histone deacetylase inhibitor activity in royal jelly might facilitate caste switching in bees)
- worker bee, queen bee, drone
- worker bee lives for about one season while queen bee lives for about 7
10
Q
What are classical nutritional studies?
A
methylation of the agouti gene
- classical example is the change in coat colour observed in progeny of yellow agouti mice exposed to methyl donors during pregnancy due to methylation of the agouti promoter
11
Q
What is chromatin architecture?
A
- organisation of over 3 billion DNA base pairs (2m) is facilitated by compaction and condensation into a complex structure known as chromatin
12
Q
What is the nucleosome?
A
- the fundamental unit of chromatin is the nucleosome
- DNA (146 bp) is wrapped around an octameric histone core consisting of two molecules each of H2A, H2B, H3 and H4
- further compacted into 30nm fibres – not well defined
- epigenetic regulation important for DNA metabolism, transcription and repair
- heterochromatin = highly condensed; inactive regions
- euchromatin = more opn chromatin conformation; active transcription
13
Q
What happens in DNA double-strand breaks?
A
- lethal lesions – unrepaired or erroneously repaired = loss of genomic integrity, carcinogenesis
- phosphorylation of the histone variant H2A.X (1/5 H2A) an early response to DNA double strand breaks
- DNA double-strand breaks occur preferentially in actively transcribing euchromatic
- error prone repair
14
Q
What are unique histone marks?
A
- can be found on different regions of a gene and may impart unique activities
e. g. - trimethylated lysine 4 on histone 3 (H3K4me3) is associated with transcriptionally active genes
- trimethylated lysine 9 on histone 3 (K3K9me3) is associated with inactive genes
- euchromatin (active transcription) and heterochromatin (inactive) is epigenetically distinguishable
15
Q
What is DNA methylation?
A
- genomic DNA may be methylated at the 5th position of cytosine, typically in the sequence of CdG; known as CpG islands
- ‘adds bulk’ to make the DNA inaccessible
- methyl groups are added by DNA methyl transferases
- heavily methylated DNA is transcriptionally inactive
