Genetics, qPCR, and Epigenetics Review

Flashcards covering phenotypic variation, complementation testing, OCA2 epistasis and pleiotropy, qPCR formulas, epigenetic mechanisms, X-inactivation, and bisulfite sequencing.

Phenotypic Variation

Variation in phenotype among individuals displaying the same trait, caused by different mutations in the same gene, mutations in different genes, or environmental factors.

Complementation Test

A genetic cross between two individuals displaying recessive mutant phenotypes to determine if the mutations are in the same gene or different genes.

Complementary Mutations

Mutations located in different genes that result in offspring with the normal phenotype when two mutant individuals are crossed.

Non-Complementary Mutations

Mutations located in the same gene that result in offspring maintaining the mutant phenotype when two mutant individuals are crossed.

OCA2 Epistasis

The ability of $OCA2$ mutations to affect melanin production, thereby masking or altering the effects of other genes involved in pigmentation.

OCA2 Pleiotropy

The ability of the single $OCA2$ gene to affect multiple distinct traits, including the pigmentation of skin, hair, and eyes.

Ct (Cycle Threshold)

The cycle in qPCR at which fluorescence rises above the threshold; a lower Ct value indicates a higher amount of starting target DNA/RNA template.

$$\Delta Ct$$

The difference in cycle threshold calculated using the formula: $\Delta Ct = Ct(\text{target gene}) - Ct(\text{reference gene})$.

$$\Delta\Delta Ct$$

The normalized cycle threshold difference calculated using the formula: $\Delta\Delta Ct = \Delta Ct(\text{sample}) - \Delta Ct(\text{control})$.

Fold Change (qPCR)

The quantitative expression change calculated using the formula: $\text{Fold change} = 2^{-\Delta\Delta Ct}$.

Epigenetic Modifications

Heritable changes in gene expression without altering the DNA sequence, mediated through DNA methylation, histone modifications, and chromatin remodeling.

DNA Methylation

An epigenetic modification adding methyl groups usually to cytosine bases at CpG sites, which generally decreases gene expression by making DNA less accessible to transcription machinery.

Histone Modifications

Epigenetic additions or removals of chemical groups on histone proteins that increase or decrease gene expression by altering the tightness of DNA packaging.

DNA Methyltransferases

Enzymes that maintain epigenetic patterns after DNA replication by recognizing methylated sites on the original strand and adding matching methyl groups to the newly synthesized strand.

Dutch Famine Birth Cohort Study

Study showing that famine exposure caused long-term epigenetic changes (DNA methylation) without changing the underlying DNA sequence, providing evidence of transgenerational epigenetic inheritance.

Xist Gene Mutation

A mutation in the $Xist$ gene on one X chromosome that prevents it from initiating X-inactivation, causing the homolog X chromosome with functional $Xist$ to undergo inactivation instead.

Bisulfite Sequencing

A technique to determine DNA methylation status where bisulfite converts unmethylated cytosines into uracils while leaving methylated cytosines unchanged.