Epigenetics & Reprogramming

A set of flashcards covering the fundamental concepts of epigenetics, chromatin modifications, and the mechanisms of cellular reprogramming and iPSC generation.

Epigenetics

Literally meaning "above" genetics, it is the study of stably inheritable phenotypes resulting from changes in a chromosome without alterations in the DNA sequence.

Epigenetic Modulation

The process by which environmental exposures, stresses, diet, and lifestyle induce chemical reactions that determine whether genes are turned on or off.

Chromatin Remodeling

The rearrangement of chromatin between a condensed state and a transcriptionally accessible state, often considered an output of histone modification.

Histone Modification

Chemical modifications such as methylation, acetylation, phosphorylation, and ubiquitination on residues of core histones $H2A$, $H2B$, $H3$, and $H4$.

DNA Methylation

A mechanism involving the transfer of a methyl group to the $C5$ position of cytosine to form $5\text{-methylcytosine}$, typically inhibiting gene expression.

Non-coding RNA

A cluster of RNAs that do not encode functional proteins but act as scaffolds, guides, or decoys to target specific epigenetic sites.

Active (Open) Chromatin

A state of chromatin associated with "switched on" genes, characterized by unmethylated cytosines and acetylated histones.

Silent (Condensed) Chromatin

A state of chromatin associated with "switched off" genes, characterized by methylated cytosines and deacetylated histones.

Cellular Reprogramming

The process of converting differentiated cells back into a pluripotent or intermediate progenitor state.

Waddington's Epigenetic Landscape

A visual model proposed in 1957 depicting the process of cell differentiation as a ball rolling down a valley into various lineages.

Induced Pluripotent Stem Cells (iPSCs)

Pluripotent cells generated from somatic cells, such as adult fibroblasts, using specific reprogramming factors.

Yamanaka's Cocktail

A specific set of reprogramming factors delivered through vectors, typically including $KLF4$, $SOX2$, $c\text{-Myc}$, and $Oct\text{-}3/4$.

Totipotent Cells

Cells found in fertilized eggs and 8-cell embryos that have the potential to differentiate into any cell type, including extra-embryonic tissues.

Pluripotent Stem Cells

Undifferentiated cells derived from the inner cell mass of a blastocyst that can give rise to all cell lineages of the body.

Transdifferentiation

The direct conversion of one differentiated cell type into another without undergoing a pluripotent intermediate state.

Somatic Cell Nuclear Transfer (SCNT)

A reprogramming method involving the transfer of a donated nucleus into an enucleated oocyte.

Stochastic Model

A model for iPSC generation proposing that the process is inefficient and involves overcoming epigenetic bumps or barriers on the differentiation slope.

p53 pathway

An important cellular barrier to reprogramming that stimulates apoptosis and reduces cell viability when reprogramming factors are overexpressed.