Chapter 17: Eukaryotic Gene Regulation

Vocabulary flashcards focusing on eukaryotic gene expression, transcription factor function, chromatin remodeling, histone variants, DNA methylation, and epigenetic inheritance based on lecture notes.

General transcription factors

Proteins required for the binding of RNA polymerase to the core promoter and its progression to the elongation stage.

Regulatory transcription factors

Proteins that regulate the rate of transcription by influencing the ability of RNA polymerase to begin transcription of a particular gene.

Activator

A regulatory protein that increases the rate of transcription by binding to a sequence called an enhancer.

Repressor

A regulatory protein that decreases the rate of transcription by binding to a sequence called a silencer.

Combinatorial control

The control of transcription by many factors, including regulatory transcription factors, small effector molecules, nucleosome arrangements, and DNA methylation.

Up-regulation

An increase in the rate of transcription, which can be $10x$ to $1,000x$, caused by an activator binding to an enhancer.

TFIID

A general transcription factor that binds the TATA box and recruits RNA polymerase II to the core promoter; its function is enhanced by activator proteins.

Mediator

A protein complex that mediates between RNA polymerase II and regulatory transcription factors, controlling whether the polymerase progresses to the elongation stage.

Glucocorticoid response element (GRE)

The specific DNA sequence that a homodimer of glucocorticoid receptors binds to in order to activate transcription.

Chromatin remodeling

The ATP-dependent modification of chromatin by protein complexes that reposition, remove, or change the composition of nucleosomes to create open or closed conformations.

DNA translocases

Components of all chromatin remodelers that move along the DNA to facilitate changes in nucleosome positioning.

Histone variants

Variations of the five standard histone genes ($H1$, $H2A$, $H2B$, $H3$, and $H4$) that play specialized roles in chromatin structure and function; humans have $70$ histone genes.

$$cenH3$$

A histone variant found at the centromere that is involved with the binding of kinetochore proteins.

$$macroH2A$$

A variant core histone abundant on the inactivated X chromosome in female mammals that plays a role in chromatin compaction.

Histone code

The pattern of covalent modifications to histone amino-terminal tails, such as acetylation, methylation, or phosphorylation, which alters chromatin conformation.

Nucleosome-free region (NFR)

A region of about $150\,bp$ located around the core promoter of many active eukaryotic genes, flanked by the $-1$ and $+1$ nucleosomes.

DNA methyltransferase

The enzyme responsible for adding a methyl group to a cytosine base, commonly occurring in mammals on $2\%$ to $7\%$ of the DNA.

CpG islands

DNA regions $1,000$ to $2,000$ nucleotides long with a high number of CpG sites, usually unmethylated in housekeeping genes but methylated in unexpressed tissue-specific genes.

de novo methylation

The highly regulated and infrequent event where specific genes are methylated in gametes from the mother or father.

Epigenetics

The study of mechanisms leading to changes in gene expression that are passed from cell to cell, are reversible, and do not change the DNA sequence.

Genomic imprinting

An epigenetic modification where one allele is silenced (e.g., maternal $Igf2$) and the other is active (e.g., paternal $Igf2$) based on DNA methylation.

X-chromosome inactivation (XCI)

The process during embryogenesis in female mammals where one X chromosome becomes a compact Barr body to ensure gene dosage compensation.

Trithorax group (TrxG)

A protein complex involved with gene activation that serves as a key regulator of epigenetic changes during development.

Polycomb group (PcG)

A protein complex (including PRC1 and PRC2) involved with gene repression during developmental differentiation.

$A^{vy}$ allele

An unusual allele of the Agouti gene in mice with a transposable element sensitive to epigenetic modifications, leading to variation in fur color based on maternal diet.

Iron regulatory protein (IRP)

An RNA-binding protein that regulates iron assimilation by binding to iron response elements (IRE) in mRNA when iron levels are low.

Iron response element (IRE)

A regulatory element found in the $5'\text{-UTR}$ of ferritin mRNA and the $3'\text{-UTR}$ of transferrin receptor mRNA.