This document discusses transcriptional control of gene expression. It begins by introducing mechanisms of gene control in bacteria and properties of RNA polymerases. It then discusses specific examples of gene regulation, including the lac operon in E. coli and enhancer control of bacterial transcription. Finally, it discusses regulatory elements in eukaryotic genes and the three nuclear RNA polymerases in eukaryotes.

1. Chap. 7 Transcriptional Control of Gene
Expression (Part A)
Topics
• Control of Gene Expression in Bacteria
• Overview of Eukaryotic Gene Control and RNA Polymerases
Goals
• Introduce the wide variety of
mechanisms used for gene
control.
• Learn the properties of RNA
polymerases.
Transcriptionally active polytene
chromosomes

2. Mutations in Transcription Factors
The protein factors that
regulate gene expression via
transcription are critical to
many biological processes.
When these factors function
incorrectly, pathological and
other aberrant effects occur
(Fig. 7.1). Examples shown
include development of the
eye in humans, wing
development in flies, and
flower development in plants.

3. Overview of Eukaryotic Transcription Control
The regulation of gene
expression, or "gene control"
is concerned with all possible
ways in which gene activity
can be controlled. While
regulation of transcription
initiation is the most common
method of control,
alternative splicing, etc. are
commonly used as well. As
shown in Fig. 7.2, control of
transcription initiation can be
achieved by activators and
repressors that modulate
chromatin condensation
state. Many other protein
factors (covered below) must
function correctly so that
transcription occurs at the
appropriate rate for proper
biological function.

4. The E. coli lac Operon
The control of gene expression by transcription activation and
repression has been studied extensively in bacteria. As an
example, the E. coli lac operon, which encodes 3 genes (lacZYA)
involved in lactose metabolism, uses both mechanisms of control
(Fig. 7.3). A specific repressor protein (the lac repressor)
inhibits transcription from the lac promoter by binding to an
adjacent DNA sequence known as the lac operator in the
absence of lactose. A general activator protein known as
catabolite activator protein (CAP) binds to a site immediately
upstream of the promoter, stimulating transcription. However,
the binding of CAP to its site requires the co-activator, cAMP,
the concentration of which is low in glucose-containing medium.
The cellular conditions under which these two regulatory proteins
bind to the lac promoter region are illustrated in the next slide.

5. Regulation of lac Operon Transcription
In the presence of glucose and absence of lactose, the
transcription of the lac operon is repressed (Fig. 7.3a). The lac
repressor is bound to the lac operator and CAP is not bound to its
control site due to low levels of cAMP. The addition of the inducer
lactose to media and its binding to the lac repressor causes the
repressor to undergo a conformational change and dissociate from
the lac operator sequence (Fig. 7.3b). However, if glucose still is
present in the medium, CAP
cannot bind to its site and
transcription is relatively low.
Finally, in the absence of
glucose and presence of
lactose, cAMP levels become
high. cAMP binds to CAP, and
the complex binds to the
control site, strongly activating
transcription by RNA
polymerase (Fig. 7.3c). E. coli
contains seven sigma factors
(e.g., s70,s54) that are needed
by RNA polymerase for
recognition of promoters and
transcription initiation. The lac
promoter requires s70, which is
the most commonly used s
factor in this bacterium.

6. Enhancer Control of Bacterial Transcription
s70 combines with RNA polymerase prior to DNA binding. The
alternative sigma factor, s54, acts very differently in that it
binds to its promoters in the absence of the polymerase. s54-RNA
polymerase further requires activators that bind to upstream
enhancer sequences for initiation. As shown in Fig. 7.4, these
"enhancer binding proteins" (e.g., NtrC) contact s54-RNA
polymerase by looping of the DNA between them. The mechanism
of transcription activation by s54-RNA polymerase is similar to
transcription activation in eukaryotes.

7. Regulatory Elements in Eukaryotic Genes
The regulation of transcription of many eukaryotic genes is highly
complex. Genes can be expressed differently in various tissues,
during different stages of development, and under different
environmental conditions. The complexity of expression of the
Pax6 gene, which is important for development of the eye and
other tissues, is illustrated in Fig. 7.7. Different versions of the
Pax6 protein are expressed in different tissues and times of
development in mouse embryos (right). Differential gene
expression is achieved via DNA regulatory sequences located
upstream, within, and even downstream of genes (left). These
regulatory sequences (promoters, enhancers, etc.) are bound by
varying sets of transcription factors in different tissues.

8. Eukaryotic R NA Polymerases
Bacteria contain only one RNA
polymerase. This enzyme has a
aIaII ß ß’ w subunit composition
(Fig. 7.11). Eukaryotes contain
three nuclear RNA polymerases
that are larger, but have core
subunits homologous to those in
the bacterial enzyme. The RPB1
subunit of RNA Pol II has a C-
terminal domain (CTD) that is
important for regulation of
transcription. The CTD contains a
7-amino-acid unit that is repeated
52 times. This sequence is
unphosphorylated prior to
initiation, but is phosphorylated on
serine and tyrosine residues after
transcription initiates. Pol I
transcribes pre-rRNA, which is
processed into the 28S, 18S, and
5.8S species. Pol II transcribes
mRNA, miRNAs, and 5 snRNAs.
Pol III transcribes tRNA, 5S
rRNA, and 1 snRNA.