Epigenetics Flashcards
What is epigenetics?
Heritable changed in a gene function that occue w/o change in DNA sequence
How is epigenetics possible?
- DNA methylation
- Histone modification (methylation/acetylation)
- Non-coding RNA
What does methylation on CpG islands indicate?
Stop signal (decreased expression of that gene)
How are the mother’s genes demethylated before blastocyte stage of development? Fathers?
Mother’s -demethylated thru dilutions
Father’s - active demethylated
@ blastocyte reestablish CpG methylation
Which nucleic acid is getting methylated in a CpG island?
Cytosine
Is de novo methylation typically seen after gastrulation?
No, rare (except in cancers)
What is an example of a gene/product downregulated thru methylation as we age?
HbF
What is Rett Syndrome?
Progressive neurloogical developmental disorder
Common causes of mental retardation in females.
1:15,000
Xlinked dominant
What causes Rett syndrome?
Mutation in MECP2 gene
Explain the pathophysiology of Rett syndrome:
- MECP2 capable of binding specificlaly to methylated DNA
- MECP2 represses transcription from methylated gene promoters
- MECP2 present ubiquitously, but mostly in brain
- LOF of MECP2 in differentiated post-mitotic neurons likely results in inappropriate overexpression of genes w/ potentially damaging effects
What are imprinted genes?
Genes that are expressed preferentially or completely from one allele depending on apwcific imprinted gene under consideration.
About 9,200 of these genes.
What happens to the epigenetic tags of imprinted genes during gamete production?
Sperm - all imprints are erased and rewritten with the paternal pattern (even genes that came from mom)
Eggs - all imprints erased and rewritten with maternal imprints.
What are the roles that imprinted genes play in development (3)?
- Embyonic growth
- Neonatal behavior
- Tissue/developmental stage specific monoallelic expression patterns.
What is the difference between Prader-Willi syndrome and Angelman syndrome?
Both include genes on chromosome 15. SNRPN / UBE3A
Prader-Willi: Mental retardation, hyperphagia
Maternal SNRPN is methylated & UBE3A is ok.
Paternal allele is deleted. (Isn’t this where the disorder lies?)
No production of SNRPN
Angelman: inappropriate laughter, seizures, mental retardation
Paternal UBE3A is methylated. Maternal alleles are deleted.
No UBE3A protein is expressed.
When are histones modified?
Post-translationally
How are histones modified?
Reversibly modified in amino-terminal tails:
- Acetylation of lysine
- Phosphorylation of serine
- Methylation of lysine/arginine
- Sumoylation
What are the closed form of histones? What else is this histone called?
Methylated
Heterochromatin
Inactive histone R group::
Acetyl
Positive charge of basic side group neutralized with addition of acetyl grp —> DNA binds less tightly
What are the epigenetic related non-coding RNA?
miRNA
SiRNA
PiRNA
IncRNA
What two IncRNAs are involved with X-chromosome inactivation?
- Xist (x-inactive specific transcript)
2. Tsix, antisense transcript (negative regulator of Xist)
Where is the Xist IncRNA transcribed from?
Xic (X inactivation center)
How does Xist silence gene expression through epigenetic modification of histones and DNA?
Xist literally covers the inactivated X chromosome.
How does Tsix regulate Xist?
Both Xist and Tsix IncRNA produce non coding RNA transcripts.
Tsix can bind to Xist sequence and inhibit it’s action (preventing the x-inactivation)
T/F- Before the X-inactivation center is established, only 1 chromosome produces Xist?
False. Pre-XIC both chromosomes are producing small amounts of Xist.
How is the XIC established?
One chromosome begins to express Tsix in high levels.
Tsix inhibits Xist and this chromosome will becomes the active X chromosome
What is phenotypic plasticity?
Ability of 1 genotype to produce more than 1 phenotype when exposed to different environments.
- Environmental stress - Hunger winter
- Adult neuronal plasticity -> mood disorders/addiction
What is an example or environmental exposure epigenetics?
Agouti gene in mice.
Should typically be methylated to silence the gene.
Thru diet modification this methylation may not occur and you will get fat yellow mice. They will be genetically identical, but epigentically different
How do we study changes in the epigenome?
- Bisulfite conversion of DNA
Sequencing, methylation specific PCR (MSP) - Methylation-sensitive restriction enzymes
Southern Blot hybridization
How does Bisulfite mediated conversion of DNA work?
Bisulfite converts C-> U if unmethylated.
Add reverse transcriptase to get complentary strand.
Use PCR/DNA sequencing/methylation specific restriction enzymes.
=> methylated C’s remain as Cs
What is an example of methylation sensitive restriction enzyme?
HpaII
