Epigenetics and Development

Our Goals:

* To build our own definition of “epigenetics”;

* To classify the major mechanisms of chromatin remodeling;

* To investigate how external environment/behaviour can trigger a completely different developmental fate

* To propose, and interpret some experiments that allow us to shed light on this phenomenon (in a specific case)

1. What could be the underlying mechanism driving the different developmental trajectory of the organisms studied in today’s class?

• Signalling pathway -> Hormones
• on/off genes -> methylation

2. a) With one or two partners, take two minutes to come up with a definition of “epigenetics”:

• Factors that influence gene expression and development that is not directly related to the pattern of nucleic acid or DNA of the individual

b) After listening to other classmates’ ideas, provide a more complete (if necessary) definition of “epigenetics”:

• Heritable modifications of DNA
• inheritance of a phenotype that is not explained by differences in DNA sequence

3. a) What are different mechanisms that can affect developmental trajectory, and that could be affected/directed by an “outside factor”?

• Methylation/acetylation
• Histone modifications and the mechanisms involved -> turn on/off areas of the genome
• The environment, for example nutrients
• Developmental pathways

b) What are the mechanisms that can affect chromatin structure?

• Chromatin remodelling factors
• Different histones
• Methylation/acetylation of histones
• Coiling of chromatin
• Methylation of DNA

4. What would you predict about gene expression patterns in the two distinct developmental trajectories if epigenetics is driving the phenotype?

• Worker bees have reproduction related genes shut down

5. Researchers (Grozinger et al., 2007) actually checked… what do you notice about the gene expression patterns in individuals following each of the two developmental trajectories?

• There is up regulation of foraging genes and down regulation of reproductive genes in worker bees, and queens bees show the opposite pattern

6. What kind of protein/factor could be a key component of the epigenetic control of developmental trajectories? How would you test your hypothesis?

• methylation -> can test with ChiP analysis, or inject methyl transferase inhibitors into larva
• Test other suspected  proteins by injection of RNAi into larva

7. What did Kucharski and colleagues find, and what does their experiment suggest?

• DNA Methyl transferases are important
• Knock down of Dnmt3 mimics royal jelly – induces queen bee development
• Workers have more of their DNA methylated

8. a) What component of the food in question is most likely to affect gene regulation?

• lipid, 10HDA, Royal Jelly Acid

b) How does the food in question activate a transcriptionally silenced gene?

• Activates Fas expression
• Overall increase in acetylation of histones when treatment with Royal Jelly acid

9. ***optional*** Using these pieces of data that we just discussed, construct a model of how consumption of the food in question leads to each of the developmental trajectories.