Lecture 8 - Epigenetics Flashcards
Every cell in the body has an identical…
genome.
How many cell types are there in humans?
Around 200 - have the same genotype but different phenotype.
What causes different cell types?
Epigenetic regulation.
Define genotype.
A collection of genes.
Define phenotype.
The sum of gene expression.
What are epigenetic modifications?
Chemical marks added to DNA and/or structures that change expression patterns of genes without altering DNA sequence – basically on/off switches.
The “switches” are different in different cell types.
What levels can be impacted by regulation of gene expression?
Transcription and translation
How can gene expression be affected during transcription?
DNA/genes need to be accessible for transcription machinery.
This can be impacted by:
- DNA organization (ex. if DNA is open or crumpled).
- DNA methylation
- Histone modification
How can gene expression be controlled during translation?
The mRNA must be stable enough to be translated. Molecules can degrade the mRNA to reduce the translation.
What is RNA interference?
Small pieces of RNA can shut down protein translation by binding to the messenger RNAs that code for those proteins.
Initiation of gene expression…
- Requires interaction of DNA with transcription factors and then RNA Polymerase (starts the process)
- DNA needs to be recognized
- Transcription factor binding needs space (easier if DNA is linear, harder if crumpled)
How is DNA organized within the nucleus?
It is crumpled, it would be too long to remain linear.
Each cell has how many meters of DNA in the nucleus?
2m
What is a nucleosome?
DNA wrapped around a histone protein. The bead-on-a-string units in chromatin.
What is chromatin?
DNA associated with histone proteins in a stable, ordered fashion.
Chromosome definition (from the slides).
In the nucleus of each cell, the DNA molecule is packaged into thread-like structures.
Heterochromatin vs. euchromatin.
Heterochromatin - Tightly packed. Inactive/condensed.
Euchromatin - Loosely packed. Active/open.
Chromatin structure is affected by…
epigenetic marks – methylation and histone modification.
Are epigenetic modifications reversible or irreversible?
Reversible
Are epigenetic modifications heritable?
Yes
Epigenetic modifications give the flexibility to…
change phenotype.
Epigenetic modifications regulate gene expression without changing…
the DNA code.
DNA methylation is found in all eukaryotic cells except…
Yeast.
What is DNA methylation?
The addition of a methyl group (CH3) to cytosine residues.
DNA methylation is _____ during cell division.
heritable
DNA methylation is influenced by…
The environment, it is non-permanent.
What is the enzyme that causes DNA methylation?
DNA methyltransferases
What is the enzyme that removes a methyl group from DNA?
DNA demethylase.
Methyl groups can be added either _____ or to maintain
_____.
Methyl groups can be added either de novo or to maintain
methylation state.
DNA methylation mainly occurs in…
CpG islands of the genome and in promoter regions.
What are CpG islands?
Regions with lots of C and G nucleotides.
DNA methylation always ____ gene expression.
Suppresses.
How can cancer be associated with DNA methylation changes?
- Less methylation of proto-oncogenes (growth factors)
- High methylation of tumor suppressor genes (pro cell death proteins like caspases).
Epigenetic silencing of canine TFPI-2 results in…
- An aggressive tumor of B-lymphocytes
- Curable in less than 10% of dogs
- Months to years for survival time
Tissue Factor Pathway Inhibitor-2 (TFPI-2)
- Enzyme, reduces activity of matrix metalloproteases (MMP)
- If MMPs are over-activated, invasive tumor growth can be promoted
What is the function of MMPs?
MMPs, among other functions, degrade extracellular matrix.
X-chromosome inactivation
- In females, one X-chromosome is tightly packed as heterochromatin (Barr body)
- Prevents the double expression of genes encoded by the X- chromosome in females
- Main mechanism: high levels of DNA methylation
Why are calico cats usually female?
- Genes for orange and black coat colour are encoded on X-chromosome
- Random inactivation of X-chromosome leads to expression of the colour encoded by the active one – mosaic expression
Are calico cats really always female?
No, XXY males can be calico but are infertile.
What is genomic imprinting?
An epigenetic phenomenon that results in the differential expression of genes depending on whether they are inherited from the mother or the father. In other words, the expression of certain genes is influenced by the parent of origin.
Typically, most genes are expressed equally from both parental alleles (gene copies), contributing equally to an individual’s traits. However, in the case of imprinted genes, one allele is selectively silenced or expressed more than the other, depending on whether it came from the mother or the father.
(sorry this is so long its from chat gpt but the slide definition sucked)
Most imprinted genes govern…
Fetal growth.
How are ligers and tigons an example of genomic imprinting?
Male lion + female tiger = liger: biggest of the big cats.
Male tiger + female lion = tigon: size comparable to parents or smaller.
Due to lifestyle and breeding strategies.
What are the breeding strategies of lions and tigers?
- Lion: competitive breeding strategy: female mates with > one male
- Tiger: non-competitive breeding strategy: female mates with one male
How is DNA charged?
Negatively
How are histones charged?
Positively
Histone composition?
Octameric protein complex with 2 molecules each of histone H3, 4, 2A, 2B
How much DNA is wound in a nucleosome?
200bp
Which histone helps with tighter packing
H1
Histones have a structured ____ and a flexible ____.
Structured core and flexible tail.
What are histone modifications?
Modifications are added to specific amino acids in the histone tails.
How many amino acids are known targets of histone modifications?
Over 60
What do histone modifications affect?
Chromatin structure. Can either activate or suppress gene expression depending on the type of modification.
Which types of histone modifications can activate transcription?
- Acetylation
- Phosphorylation
- Methylation
- Ubiquitylation
What histone modifications can repress transcription?
- Methylation
- Ubiquitylation
- Sumoylation
Which histone modifications can either activate or repress transcription?
Methylation and ubiquitylation
What factors impact the context of histone modifications?
- Position of modification
- Interaction with DNA
Tasmanian devil facial tumor disease
- Infectious tumors around the mouth of Tasmanian devils
- Interferes with feeding, causes starvation
- Transmission of cancer cells by biting, feeding on carcasses, sharing of food
- Detected 1996, in 2015 95% of affected populations were wiped out
Why are tumor cells not recognized by immune system?
- When ‘foreign’ cells enter the body, immune reaction destroys those cells which requires the expression of major histocompatibility complex (MHC)
- One study showed that tumor cells have reduced histone acetylation (which
activates gene expression) in gene encoding a subunit of MHC - No recognition by immune system of host as a result
What are non-coding RNAs?
RNA transcribed from the genome that does not encode for proteins
What are regulatory non-coding RNAs?
Involved in the regulation of mRNA/translation
What are the different types of non-coding RNAs?
- MicroRNAs (miRNA)
- Small interfering RNAs (siRNA)
What is the mechanism of non-coding RNA called?
RNA interference (RNAi)
What is the mechanism for siRNA interference?
- Specific for one mRNA transcript (no mismatches)
- Induces mRNA cleavage
What is the mechanism for miRNA interference?
- Can target multiple mRNAs (mismatches)
- Binds mostly 3’ UTR
- mRNA degradation and cleavage
- T ranslational repression, ‘storage’ and translation at a later time point
- Control 60% of all protein
encoding genes
How is miRNA used in cows to control milk quality?
miRNA-152 regulates expression of DNA methyltransferase involved in the development and lactation process in mammary glands.
- Global DNA methylation decreased
- Lactation - related gene expression (casein, triglyceride, lactose secretion
higher) = high quality milk.
Cows with high quality milk have ____ methylation.
Less
What environmental factors influence epigenetic modifications?
- Nutrition
- Alcohol
- Stress
- Drugs
- Age
- Pollutants
- Pathogens
How do epigenetic tags change as twins age?
They become more different.
Agouti viable yellow (Avy) mouse model as epigenetic
sensor:
The Avy gene is sensitive to methylation. Low methylation will result in a yellow colour of the mouse and high methylation will be more brown (pseudo-agouti).
What is genistein and how does it affect methylation?
Major ingredient of soy, donor of methylgroups
What is EWAS?
Epigenome-wide association studies (EWAS)
How is EWAS done?
- Bisulfite conversion: Single-stranded DNA is treated with sodium bisulfite
- Unmethylated cytosine is converted to uracil, methylated C is not affected
- Products upon amplification contain unconverted cytosine at methylated positions and thymidine instead of previously unmethylated cytosines
- Hybridization on chip and colour read out for methylated/unmethylated DNA
