Epigenetics and How We Study It

Vocabulary flashcards covering foundational terms, enzymes, techniques, and disease links presented in the lecture on epigenetics and its experimental study.

Epigenetics

Heritable changes in phenotype that alter gene expression without changing the DNA sequence.

Histone

A protein around which DNA is wrapped to form nucleosomes, helping package chromosomes and regulate gene access.

Histone Tail

The N-terminal extension of a histone protein that can be post-translationally modified to influence chromatin structure.

Chromosome

A DNA–protein structure carrying genetic information; packaged with histones and subject to epigenetic regulation.

Stem Cell

An undifferentiated cell capable of self-renewal and differentiation into specialized cell types.

Gene Regulation

Control of the timing, location, and amount of gene expression within a cell.

Population Stratification

Differences in allele frequencies between subgroups, relevant when interpreting genetic and epigenetic studies.

Gene Dosage

The number of copies of a gene present in a cell and its effect on phenotype, e.g., trisomy 21.

Trisomy 21

Presence of three copies of chromosome 21; causes Down’s syndrome and increases APP gene dose.

Amyloid Precursor Protein (APP)

A gene on chromosome 21 whose overexpression is linked to Alzheimer’s disease in Down’s syndrome.

X Chromosome

A sex chromosome containing >1,000 essential genes; dosage balanced by X-inactivation.

X-Inactivation

Random silencing of one X chromosome in female cells to equalize gene dose with XY males.

X-Linked Variegation

Mosaic expression pattern caused by random X-inactivation in precursor cells.

Epigenetic Mark

A chemical modification such as DNA methylation or histone modification that alters chromatin state.

DNA Methylation

Addition of a methyl group to cytosine, usually at CpG dinucleotides, often leading to gene repression.

CpG Island

A 500-1500 bp DNA region rich in CG dinucleotides frequently located at gene promoters.

Promoter

DNA sequence upstream of a gene where transcription factors and RNA polymerase initiate transcription.

DNA Methyltransferase (DNMT)

Enzyme family that installs methyl groups on DNA cytosines.

DNMT1

Maintenance methyltransferase that copies existing methylation patterns during DNA replication.

DNMT3A

De novo DNA methyltransferase that establishes new methylation marks independently of template strand.

DNMT3B

Another de novo DNA methyltransferase important for establishing new methylation patterns.

5-Methylcytosine (5mC)

Methylated form of cytosine that commonly represses gene expression at promoters.

5-Hydroxymethylcytosine (5hmC)

Oxidized derivative of 5mC produced by TET enzymes; enriched in stem cells and neurons.

TET Enzymes

Ten-eleven translocation dioxygenases that oxidize 5mC to 5hmC, 5fC, and 5caC.

Hemimethylated DNA

DNA in which only one strand is methylated; substrate for DNMT1 during replication.

Methyl-CpG-Binding Domain Proteins (MBD)

Proteins that bind methylated CpG sites and recruit repressive chromatin modifiers like HDACs.

Histone Deacetylase (HDAC)

Enzyme that removes acetyl groups from histone tails, condensing chromatin and repressing transcription.

Transposable Element

Mobile DNA sequence whose activity is suppressed by DNA methylation to maintain genome stability.

Intra-cisternal A-Particle (IAP)

A retrotransposon whose insertion upstream of the agouti gene creates a cryptic promoter in Avy mice.

Agouti Gene

Mouse gene controlling coat color; ectopic expression by an IAP affects obesity and diabetes risk.

Gene–Environment Interaction

Influence of environmental factors (e.g., diet) on gene expression through epigenetic mechanisms.

Methyl-Donor Diet

Diet rich in folate, B12, choline, betaine that increases DNA methylation levels in offspring.

Restriction Fragment Length Polymorphism (RFLP)

Variation in DNA fragment sizes after enzyme digestion used to detect genetic differences.

Methylation-Sensitive Restriction Enzyme

Endonuclease whose cutting ability depends on the methylation status of its recognition site.

Methylated DNA Immunoprecipitation (MeDIP)

Technique that enriches methylated DNA using 5-mC antibodies for sequencing or microarray analysis.

Bisulfite Conversion

Chemical treatment that deaminates unmethylated cytosine to uracil, enabling methylation mapping.

Polymerase Chain Reaction (PCR)

Enzymatic amplification of DNA; primers must match bisulfite-converted sequences for methylation assays.

Pyrosequencing

Sequencing-by-synthesis method that detects pyrophosphate release; quantifies percent methylation at CpG sites.

Primer Dimer

Unwanted PCR product formed by primers annealing to each other, hindering sequencing accuracy.

Nanopore Sequencing

Single-molecule sequencing that measures changes in ionic current; can directly detect methylated bases.

SMRT Sequencing

PacBio Single Molecule Real-Time sequencing that infers base modifications from altered incorporation kinetics.

Cancer Epigenetics

Study of DNA methylation, histone changes, and miRNA alterations driving tumor initiation and progression.

Hypermethylation

Excessive promoter CpG methylation that often silences tumor suppressor genes in cancers.

Hypomethylation

Genome-wide loss of DNA methylation linked to chromosomal instability and oncogene activation.

Tumor Suppressor Gene

Gene that inhibits cell proliferation; epigenetic silencing contributes to tumorigenesis.

Oncogene

Gene whose overactivation promotes cancer; can be unleashed by hypomethylation or chromatin changes.

Biomarker

Measurable molecular indicator (e.g., DNA methylation pattern) used for diagnosis or therapy monitoring.

Genomic Instability

Increased frequency of mutations and chromosomal alterations often associated with global hypomethylation.