Genome Evolution and Genome Packaging Vocabulary

Vocabulary flashcards covering topics on genome evolution, intron origin hypotheses, exon shuffling, histone modifications and packaging, nucleosome positioning, and telomere/telomerase biology.

Introns Early Hypothesis

The hypothesis proposing that genes were always interrupted by introns and that prokaryotes later evolved strategies to eliminate them while eukaryotes retained them.

Introns Late Hypothesis

The hypothesis proposing that ancestral genes started as uninterrupted sequences and that introns later invaded the genomes of eukaryotic organisms.

Exon Shuffling

The evolutionary process in which exons are moved to new regions of the genome via meiotic recombination or transposon activity, creating novel gene structures.

Protein Domain

A distinct, conserved structural and functional subunit of a protein that can fold and function independently and is often encoded by a single exon.

Gene Trap

An experimental technique in which an artificial exon encoding GFP is randomly inserted into introns of host genomic DNA to tag and track endogenous protein expression.

Green Fluorescent Protein (GFP)

A reporter domain adapted from the jellyfish Aequorea victoria that fluoresces green under UV light, allowing visualization of transgene expression in live cells.

Pseudogenes

Non-functional copies of genes arising from duplication events or retrotransposition that are typically neither transcribed nor translated.

Histone Octamer

An eight-protein complex consisting of two $H2A\text{--}H2B$ dimers and one $H3_2H4_2$ tetramer that forms the core particle around which DNA wraps.

Nucleosome

The basic repeating unit of eukaryotic chromatin, consisting of approximately $147\,bp$ of DNA wrapped $1.65$ times around a core histone octamer.

Linker DNA

The less compacted segments of DNA situated between adjacent nucleosomes, which are frequently bound by linker histone H1.

Histone H1

A linker histone protein that binds to linker DNA outside the core nucleosome particle to promote higher-order chromatin packaging.

Histone Acetylation

The addition of an acetyl group to lysine residues on histone N-terminal tails, which neutralizes positive charge, decreases histone-DNA binding, and promotes gene expression.

Histone Acetyltransferases (HATs)

Enzymes that add acetyl groups to lysine residues on histone tails, loosening chromatin structure to facilitate transcription.

Histone Deacetylases (HDACs)

Enzymes that remove acetyl groups from lysine residues on histones, restoring positive charge and repressing gene transcription.

Histone Methylation

The addition of methyl groups to lysine or arginine residues on histones by methyltransferases, maintaining the positive charge on histones and frequently associated with heterochromatin.

Histone Phosphorylation

The addition of a phosphate group to serine or threonine residues on histones by kinases, introducing a negative charge that creates electrostatic repulsion with DNA.

Bromodomain

A specialized protein domain that specifically recognizes and binds to acetylated lysine residues on histone tails.

Chromodomain

A specialized protein domain that specifically recognizes and binds to methylated lysine residues on histone tails.

FACT (Facilitates Chromatin Transcription)

A histone chaperone protein complex that loosens $H2A\text{--}H2B$ dimers from nucleosomes during transcription to allow RNA polymerase passage.

Phased Nucleosomes

Nucleosomes positioned non-randomly at specific locations on DNA to prevent or allow the reading of particular genomic regions.

Translational Positioning

The linear position of a DNA sequence relative to the boundaries of the histone octamer particle.

Rotational Positioning

The exposure of DNA on the surface of the nucleosome, describing which base pairs face outward versus inward toward the octamer.

DNase I Hypersensitive Sites

Nucleosome-free regions of chromatin, such as active promoters or enhancers, that are accessible and highly vulnerable to digestion by DNase I.

Telomere

A region of short tandem repetitive nucleotide sequences at the end of a linear eukaryotic chromosome that protects against end-degradation and chromosomal fusion.

Telomerase

A ribonucleoprotein reverse transcriptase enzyme containing an RNA template (TERC) and catalytic protein subunit (TERT) that extends the $3'$ end of telomeric DNA.

T-Loop

A large loop structure formed when the single-stranded $3'$ telomeric overhang loops back and invades double-stranded chromosomal DNA.

D-Loop (Displacement Loop)

A triple-stranded region formed inside a T-loop where the single-stranded $3'$ overhang displaces one strand of double-stranded telomeric DNA.

Shelterin Complex

A six-protein complex comprising TRF1, TRF2, Rap1, TIN2, TPP1, and POT1 that coats telomeres and protects chromosome ends from DNA damage pathways.

TRF2 (Telomere Repeat Binding Factor 2)

A key subunit of the shelterin complex that catalyzes the formation of the T-loop and D-loop structures at linear telomeres.