Chapter 16 Gene Regulation in Eukaryotes
Outline
I. The use of genetics to study gene regulation
A. The analysis of regulatory components focuses on mutations that affect a gene’s function but
do not affect the amino acids in the gene’s product
1. Regulatory mutations that map at or near the gene help define cis-acting DNA sequences that
influence transcription
2. Regulatory mutations that map far from a target gene help define trans-acting genetic elements
II. Most gene regulation occurs at the initiation of transcription
A. In eukaryotes, three RNA polymerases transcribe different sets of genes
1. RNA polymerase I is responsible for the transcription of rRNA
2. RNA polymerase III transcribes the tRNAs and other small RNAs
3. RNA polymerase II transcribes all protein-encoding genes
4. Cis-acting regulatory regions recognized by pol II consist of a promoter and one or more
enhancers
B. Trans-acting proteins control transcription from class II promoters
1. Basal factors are required to maintain a basal level of transcription
2. Activators bind to enhancer sequences and increase transcription 100-fold above the basal level
3. Most eukaryotic activators function as dimers
4. Repressors diminish transcriptional activity
5. The myc-max system is a regulatory mechanism for switching between the activation and
repression of transcription
6. The yeast GAL system is another complex regulatory mechanism
D. A locus control region (LCR) is a cis-acting regulatory sequence that operates on a cluster of
related genes
E. Complex regulatory regions allow an organism to fine tune gene expression
F. Chromatin structure plays a role in eukaryotic gene regulation
1. The normal structure of chromatin provides a brake on run-away basal transcription
2. The remodeling of chromatin mediates the activation of transcription
3. Hypercondensation over chromatin domains causes transcriptional silencing
4. Genomic imprinting results from chromosomal events that selectively silence the expression of
genes inherited from one parent or another
III. Regulation after transcription influences RNA production, protein synthesis, and protein
stability
A. RNA splicing helps regulate gene expression
B. RNA stability provides a mechanism for controlling the amount of gene product synthesized
C. mRNA editing can affect the biological properties of a gene’s product
D. Noncoding sequences in mRNA can help modulate translation
E. Protein modifications after translation provide a final level of control over gene function
1. Ubiquitination targets proteins for degradation
2. Phosphorylation and dephosphorylation are other regulators of protein activity
IV. Sex determination in Drosophila: a comprehensive example of gene regulation
A. The X/A ratio regulates expression of the sex lethal (Sxl) gene
1. Numerator subunit homodimers may function as transcription factors that turn on Sxl
2. The Sxl protein expressed in early development in females regulates its own later embryonic
expression through RNA splicing
3. The effects of Sxl mutations
4. To summarize: The Sxl gene acts as an on/off switch that is sensitive to the X/A ratio
B. Sxl triggers a cascade of splicing
1. Effects of mutation in tra
C. The dsx-F and dsx-M proteins are transcription factors that determine somatic sexual
characteristics
1. The effect of dsx mutations
D. The Tra and Tra-2 proteins also help regulate expression of the Fruitless gene
E. Summary: a complex network of molecular interactions regulates the determination of somatic
sexual characteristics in Drosophila
Essential Concepts

The activity of most genes in eukaryotic cells is regulated primarily at the point of
transcriptional initiation. Analyses of mutations that affect a gene’s function without
changing the sequence of its product provided insight into this level of regulation. Through
these mutations, researchers defined cis-acting DNA regulatory elements and trans-acting
transcription factors.

The eukaryotic genome contains three classes of genes, each associated with a different type
of promoter and transcribed by a different RNA polymerase. Class I genes encode the
rRNAs. Class III genes encode the tRNAs as well as other small RNA molecules. Class II
genes, by far the largest class, encode all proteins.

Two types of cis-acting regulatory regions -- promoters and enhancers -- are associated with
class II genes. All promoters are located at the 5’ end of the gene they influence. The
enhancers have a more variable location in relation to the genes they control.

The binding of non-specific basal factors to promoters is a prerequisite for the transcription of
a gene. Basal factors alone allow a low, nonspecific basal level of gene transcription.

The specific interactions of transcription factors with enhancer elements can increase
transcriptional initiation above the basal level. Activation is mediated by transcription factors
called activators that bind to enhancers and interact with basal factors at the promoter.
Activation can be modulated by repressor proteins that compete with activators for enhancer
binding or quench the ability of activators to carry out their function. Many activators and
repressor form homodimers and/or heterodimers. Formation of these dimers is a prerequisite
for them to function as transcription factors.

Although promoters and enhancers are the most common and best characterized types of cisacting regulatory elements, there are other elements that do not fit into either of these classes.
One such element is the Locus Control Region associated with the -globin gene cluster.

The regulation of transcription is a complex process dependent on the interactions of multiple
enhancer elements with many competing transcription factors, and responsive to signals
originating within and outside the cell. The integration of signals and regulatory components
determines the precise level of transcription of a particular gene in a particular cell at a
particular time.

The structure of chromatin around a gene contributes to the regulation of transcription.
Normal chromatin structure prevents run-away transcription from genes that are not under
activation. The unraveling of the DNA in chromatin is an initial step in activation.
Hypercompaction of chromatin domains causes transcriptional silencing by blocking access
tot he promoter and enhancers of a gene and thereby preventing its activation even in the
presence of activator proteins.

Genomic imprinting is an example of epigenetic control over gene expression. Imprinting
operates on the copy of a gene received from one parent but not the other. DNA methylation
plays a role in the maintenance of imprinting from one mammalian generation to the next.

Although the regulation of most genes depends primarily on controls over transcription, in
some cases, further regulation down the path to protein production also plays a role.
Modulation of gene function can occur through changes in RNA splicing or RNA stability,
mRNA editing, changes in the efficiency of translation, and chemical modification of the
gene product.