Epigenetics Flashcards
Define epigenetics
Anything other than DNA used to control inheritance of genetic information.
Name four modes of genetic inheritance through epigenetics
- DNA methylation
- modification of histone proteins
- non-coding RNAs
- chromatin remodelling
At what location is DNA methylated?
At CpG
When are DNA methylation patterns established?
During embryo development, and are maintained by copying mechanisms during cell replication
Describe the writers of DNA methylation.
DNA methyltransferases: dnmt3a and dnmt3b perform de novo methylation, and dnmt1 performs maintenance methylation
What are CpG islands?
Short stretches of DNA in which the frequency of CpG methylation is higher.
Describe DNA hypo- and hypermethylation.
Hypomethylation: less methylation, more expression.
Hypermethylation: more methylation, less expression (txn factors cannot bind)
Define and describe the readers of DNA methylation.
These proteins have a conserved methyl-binding domain as well as a variable transcriptional repression domain.
What is MeCP2?
It regulates transcription as a reader of DNA methylation. Depending on the types of proteins that bind to it, it can both activate and supress gene expression in neurodevelopment.
What is Rett Syndrome?
It is a disorder caused by mutations in MeCP2 methylation reader. It is an X-linked neurodevelopment disorder.
Describe DNA methylation erasers.
They are involved in passive or active DNA demethylation and include the TET (ten-eleven translocation) family enzymes.
What is active DNA demethylation?
It involved three different enzymes to carry out DNA repair:
- methylcytosine is hydroxylated by TET to form hydroxymethylated cytosine
- methylcytosine is deaminated by AID to form methyluracil
- these intermediates can be replaced with cytosine by BER
What are three roles for DNA methylation?
- gene silencing
- X-chromosome inactivation and genomic imprinting
- environmental factors induce epigenetic changes, leading to cancer
How does DNA methylation lead to cancer?
- Hypomethylation results in genome instability
- hypermethylation can silence tumor suppressor genes
- methylation sites are hotspots for C->T transitions
- methylation increases binding of chemical carcinogens and increase UV-induced mutations
How does methylation occur?
S-adenosyl methionine is formed by methionine and ATP and adds a methyl group to 5’ carbon of cytosine with the help of DNMTs.
What is the source of methyl groups for DNA methylation?
- flavenoids and soft fruits and soya inhibit DNMT and could help reverse hypermethylation to tumor suppressor genes!
- folates regulate methylation
- diet during early development can cause lasting changes into adulthood.
How does BPA affect DNA methylation?
Mice fed BPA had unhealthy babies, but when supplemented with folate rich foods, the babies were born healthy.
How do father’s diets affect DNA methylation and epigenetics?
Food availability to paternal grandfathers at a young age affects the lifespan of his children.
Shortage of food = longer lifespan. More food = shorter lifespan and death by cardiovascular disease or diabetes.
Nutritional info about environment captured and passed onto next generations!
Describe the drastic role of DNA methylation in honeybees.
- Queen been larvae feed on rolly jelly secreted by worker bees
- queens are fertile and behave differently, while workers are sterile (over 550 genes affected)
- both castes have same genome
- a DNMT3 denovo patterning on larvae in a jelly-like manner caused them to develop into queens
Compare and contrast maternal and paternal genomic imprinting.
Gene inherited from one parent is permanently inactivated and is passed on in this condition. Monoallelic inheritance.
- maternal imprinting: allele from mother is inactive. only dad’s allele is expressed.
- paternal imprinting: allele from father is inactive. only mom’s allele is expressed.
On which chromosomes are most imprinted genes found?
Despite X-chromosome barr bodies, most imprinted genes are on the autosomes.
Describe the inheritance of insulin-like growth factor 2 (Igf2) in mice.
- only the paternal allele is expressed (mom’s is silenced)
- inheritance of mutant maternal allele has no affect
- if mutant paternal allele is inherited, mouse will experience dwarfing
Describe the different histone subunits.
Histone core made of H2A, H2B, H3, H4. Linker is H1.
How can histones hold large amounts of information?
There are about 44 lysines on the tails of histones that can possibly be acetylated!
Name the types of histone modification.
- acetylation
- methylation
- phosphorylation
- ubiquitination
Is euchromatin acetylated or deacetylated?
It is loosely packed, so it is highly acetylated.
Is histone methylation activating or repressing?
It can be either, depending on the location and the context.
What are the two main classes of HAT’s?
- nuclear
- cytoplasmic
specificities are defined in vitro
Describe sex-linked histone acetylation and the experiment supporting it.
- male rats left to self-administer cocaine or saline.
- cocain-sired male rats developed cocaine resistant phenotype, but no affect on females
- saline-sired males had normal histone acetylation levels
- cocaine-fed males and their sons had elevated acetylation at Bdnf promotor causing higher Bdnf expression
What is the effect of HDAC inhibitors?
- can induce acetylation of histones
- can inhibit tumor growth (tumor suppressor genes can remain expressed)
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Describe the role of readers in histone acetylation.
They bind acetylated lysine tails and recruit txn factors and chromatin organizers required for txn initiation and elongation,
What is the goal of epigenetic editing?
Targeted overwrite of epigeneitc marks to modulate expression of selected target genes.
What type of chromatin do embryonic stem cells have?
Fully open, ready for de novo epigenetic modification.
What is the epigenome project?
It elicidates the relationship between genetic and epigenetic variation and its impact on health.
What is the major challenge to epigenome mapping?
- there is no single epigenome
- each cell type has its own array of epigenetic marks
Why should mother rats lick their babies?
- highly nurtured pups grow up to be calm adults, nonlicked pups are anxious as adults
- the difference is epigenetic and is stable into adulthood
- shows epigenetic memory
What types of noncoding RNAs are involved in epigenetics?
lncRNAs and miRNAs
Define lncRNA
transcripts >200nt in length that do not contain ORFs capable of translating proteins.
What is the evidence of lncRNA functionality?
- tissue and stage specific expression
- deregulated expression in disease
What are the mechanisms of action of lncRNAs?
- chromatin remodeling
- regulation of RNA txn, splicing, editing, transport, translation, degradation, and compartmentalization
What is the role of Xist in chromosome inactivation?
Xist mediates inactivation of female X chromosome. It coats the chromosome in cis, and is expressed only from the inactive X chromosome.
- Xist recruits polycomb repressive complex 2 (PRC2)
- PRC2 marks chromatin with repressive histone modifications
What is the function of Tsix?
It is antisense to Xsist and serves as an antagonist of Xist expression. Its expression demarcates the active X chromosome.
What is the role of miRNAs in epigenetics?
They regulate gene expression post-transcriptionally by binding 3’ UTR of specific mRNAs.
How are miRNAs used as biomarkers?
extracellular miRNAs in blood, serum, plasma, saliva, and urine have been associated with various pathological conditions including cancer
How are miRNAs not degraded in extracellular space?
They are delivered in exosomes to recipient cells.
What are exosomes and when are they released?
- Small extracellular vesicles
- come from early endosomal pathway
- inward budding of endosomal membrane gives rise to cytosolic multivesicular bodies
- exosomes are released when MVBs fuse with the plasma membrane.
What types of molecules are contained in exosomes?
proteins, lipids, mRNAs, miRNAs. lipid bilayer protects these things from degradation
What are the steps of miRNA transfer by exosomes?
- miRNA packaging into exosomes and MVB formation
- exosome release from donor cell
- exosome uptake by acceptor cell
How can exosomes be both good and bad?
They can deliver molecules such as prions that cause Alzheimer’s disease. They can also be used therapeutically by removing exosomes from a patient, loading them with a drug, and delivering back to patient for a higher immune system tolerance.
