Lecture 9 Notes: Epigenetics, X-inactivation, and RNA Modification

Exam grades are available on Canvas.
The mean score was approximately 67.
Students above the mean should continue their current study habits.
Students below the mean should adjust their approach.
Exam 3 will be the same length as Exam 2 but with twice the time allotted.
The focus should be on understanding, synthesizing, and applying the material.
Utilize available resources such as TAs and office hours.
The course requires applying knowledge to new situations.
The final grade is based on three exams and quiz sections, with an average around 3.1 or 3.2.
Address any issues with the instructor or TAs.

Exam 3 will cover lectures 7 through 13.
It's important to understand concepts from lectures 1 through 6, such as epigenetics.

One of the X chromosomes in female cells is transcriptionally silenced (Xi).
Calico cats are a visual example of X inactivation.
Patches of different colors (e.g., black and orange) result from different X chromosomes being inactivated in different cells.
Mechanism involves epigenetic modifications.
X inactivation is an early developmental process in mammalian females.
One X chromosome is transcriptionally silenced, with most RNA expression suppressed.
Requires the X inactivation center (XIC).
In a random manner, XIC gets activated in one X chromosome but not both.

One X chromosome gets crumpled and packaged to prevent transcription.
Inactivation can be either the paternal or maternal X chromosome in different cells.
Once a chromosome is inactivated, that state is inherited in cell division.
Females are mosaics, with patches of cells having different active X chromosomes.
X inactivation is random.
Once inactivated, it creates a clonal batch of cells with the same X chromosome inactivated.
Dosage compensation: Females have one X inactivated to have a similar amount of X-linked gene expression as males.

Females are mosaics due to random X inactivation.
This can result in females being carriers of X-linked diseases without showing symptoms.
Color blindness: Genes for color perception are on the X chromosome, so women can be carriers if they have a mutated recessive allele on at least one of their X chromosomes.
Rett Syndrome: Mutation in MECP2 (methyl CpG binding protein 2) causes a neurodevelopmental disorder.
Females with Rett syndrome can show symptoms.
Therapy opportunity: Reactivating the silenced copy of the X chromosome.
X chromosome inactivation begins at the Xist center.
The long non-coding RNA coats the X chromosome, recruiting epigenetic machineries such as histone methylation and DNA methylation.

Cloning Puja's cat, Xisti, resulted in a different coat color in the clone, Xisti 2.
Possible explanation: Random X chromosome inactivation.
Xisti 2 is female.
Males with two X chromosomes (Klinefelter syndrome) also exhibit X inactivation.

Kathy Carrico and Drew Weissman won the Nobel Prize for their work on mRNA vaccines.
Problem: Introducing mRNA into cells triggered a strong immune response (interferon pathway).
Solution: Modified mRNA with pseudouridine instead of uridine.
Pseudouridine modification prevents immune system activation, increases mRNA stability, and reduces side effects like fever and muscle aches.
COVID-19 vaccines used pseudouridine-modified mRNA.

ADAR enzymes modify RNA bases, including methylation and deamination.
ADAR changes the coding sequence in RNA (unlike other epigenetic modifications).
ADAR converts adenosine to inosine, which is read as guanosine.
Thousands of genes are modified by ADAR in the human genome.

ADAR deaminates adenosine in a codon CHG in the AMPA glutamate receptor mRNA.
This is essential for proper receptor function.
The ADAR enzyme recognizes double-stranded RNA structures.
Normally, ADAR changes glutamine to arginine in the pore of the channel, allowing sodium to pass.
If ADAR doesn't work (e.g., due to a mutation), glutamine remains in the pore, allowing calcium to enter the cell.
Excessive calcium leads to exotoxicity and epileptic seizures.