Chapter 12 Control of Genetic information via Gene regulation

Chapter 12 – The Control of Genetic Information via Gene
Regulation
Chapter Outline
1. Overview of gene regulation
2. Regulation of transcription
in bacteria
3. Regulation of transcription
in eukaryotes: roles of
transcription factors
4. Regulation of transcription
in eukaryotes: changes in
chromatin structure and
DNA methylation
5. Regulation of RNA splicing
and translation in
eukaryotes

12.1 Overview of Gene Regulation
Section 12.1 Learning
Outcomes
1. Discuss the various ways
that organisms benefit from
gene regulation (in other
words, what can organisms
do because they have gene
regulation)
2. Identify where gene
regulation can occur in the
pathway of gene expression
for bacteria and eukaryotes

12.1 Overview of Gene Regulation
• Gene regulation refers to the ability of cells to control the
expression of their genes
• Most genes are regulated to ensure proteins are produced at
the correct time and in the correct amount
• Regulation conserves energy by producing only what is needed
• Some genes have relatively constant levels of expression; such
constitutive genes frequently encode proteins that are constantly
required (like enzymes for carbohydrate metabolism)
• Many proteins regulate gene expression
through binding to DNA

12.1 Overview of Gene Regulation
Bacteria Regulate Genes in Response to Changes in
Their Environment
• The bacterium Escherichia coli can use many types of sugars as
food sources, which increases its chances of survival
• In order to utilize lactose, E. coli cells need a transporter and an
enzyme that catalyzes the breakdown of lactose
• When lactose is not
present, the cell
makes very little of
these proteins
• However, when
lactose becomes
available gene
regulation directs
increased expression
of these proteins

12.1 Overview of Gene Regulation
Eukaryotic Gene Regulation Produces Different
Cell Types in a Single Organism
• Cell differentiation is the process by which cells become
specialized into particular types
• The skeletal muscle cell, neuron, and skin cell shown below all
contain the same genome, however the proteome of each cell is
quite different due to gene regulation
• Both the types of proteins as well as the quantity of specific
proteins are important differences between cell types

12.1 Overview of Gene Regulation
Eukaryotic Gene Regulation Enables Multicellular
Organisms to Proceed Through Developmental Stages
• For multicellular organisms that progress through developmental
stages, certain genes are expressed at particular stages
• For example, the expression of hemoglobin subunits changes
during embryonic, fetal, and newborn developmental stages
• Embryonic and fetal forms of
hemoglobin have a higher
affinity for oxygen than adult
hemoglobin, which allows the
developing offspring to take
oxygen from the maternal
bloodstream

12.1 Overview of Gene Regulation
Eukaryotic Gene Regulation Enables Multicellular
Organisms to Proceed Through Developmental Stages
• A functional hemoglobin protein is composed of 4 globin subunits
• During the embryonic stage, the epsilon (ε)- and zeta (ζ)-globin
genes are “turned on”
• At the fetal stage, the embryonic genes are “turned off” and the
alpha (α)- and gamma (ᵯ )-globin genes are “turned on”
• At birth, the ᵯ –globin gene is
“turned off” and the beta (β)-
globin gene is “turned on”
• Gene regulation ensures that
the correct hemoglobin protein
is produced at the right time in
development

12.1 Overview of Gene Regulation
Gene Regulation Occurs at Different Points in the
Process from DNA to Protein
• For protein-encoding genes
in bacteria, gene expression
can be regulated during
transcription, translation,
or post-translation (ex:
feedback inhibition of
enzymes)
• For protein-encoding genes
in eukaryotes, gene
expression can be regulated
during transcription, RNA
modification, translation, or
post-translation

12.2 Regulation of Transcription in Bacteria
Section 12.2 Learning
Outcomes
1. Explain how regulatory
transcription factors and
small effector molecules are
involved in the regulation of
transcription
2. Diagram the organization of
the lac operon
3. Explain, in detail, how the
lac operon is regulated by
negative and positive control
4. Predict the rate of
transcription for given levels
of lactose and glucose

12.2 Regulation of Transcription in Bacteria
Transcriptional Regulation Involves Regulatory
Transcription Factors and Small Effector Molecules
• Regulatory transcription factors, proteins that bind to regulatory
sequences in DNA, are frequently used to change levels of gene
expression
• Repressors are transcription factors that exert negative control
and decrease transcription
• Activators are transcription factors that exert positive control
and increase transcription

12.2 Regulation of Transcription in Bacteria
Transcriptional Regulation Involves Regulatory
Transcription Factors and Small Effector Molecules
• Transcriptional regulation also involves small effector molecules
• Small effector molecules bind repressors or activators, causing a
change in their conformation and function

12.2 Regulation of Transcription in Bacteria
The lac Operon Contains Genes That Encode Proteins
Involved in Lactose Metabolism
• An operon is a cluster of genes that is under transcriptional control
of one promoter; operons are found in bacterial chromosomes
• An operon allows the coordinated regulation of a group of genes
with a common function; transcription produces a polycistronic
mRNA that encodes more than one polypeptide
• In E. coli, the lac operon contains genes for lactose metabolism

12.2 Regulation of Transcription in Bacteria
The lac Operon Contains Genes That Encode Proteins
Involved in Lactose Metabolism
• The lac operon includes
the promoter (lacP),
three structural genes
(lacZ, lacY, lacA), the
operator (lacO) which is
a repressor binding site,
and the CAP site which is
an activator binding site

12.2 Regulation of Transcription in Bacteria
The lac Operon Is Under Negative Control
by a Repressor Protein
• The lacI gene encodes the lac repressor, and it is constitutively
expressed at a low level
• In the absence of lactose, the lac repressor binds the operator and
prevents RNA polymerase from transcribing the structural genes

12.2 Regulation of Transcription in Bacteria
The lac Operon Is Under Negative Control
by a Repressor Protein
When E. coli is exposed to lactose:
1. A small amount of lactose is transported into the cytoplasm via
lactose permease, and some is converted to allolactose by the
β-galactosidase enzyme
2. Allolactose levels rise and allolactose
(a small effector) binds to the lac
repressor, causing a conformational
change that prevents the repressor
from binding the operator
3. RNA polymerase transcribes the lacZ,
lacY, and lacA genes at a high rate
4. Translation produces associated
proteins

12.2 Regulation of Transcription in Bacteria
The lac Operon Is Under Negative Control
by a Repressor Protein
• Regulation of the lac operon allows E. coli to conserve energy,
making proteins for lactose utilization only when needed
• The lac operon is inducible (normally “off”, turned “on” as needed)
and allolactose is an inducer (effector that increases transcription)

12.2 Regulation of Transcription in Bacteria
The lac Operon Is Also Under Positive Control
by an Activator Protein
• CAP (catabolite activator protein) is an activator of the lac operon
• CAP is controlled by a small effector,
cyclic AMP (cAMP), which is produced
from ATP
• The cAMP-CAP complex binds to the CAP
site and enhances the ability of RNA
polymerase to bind the promoter
• The level of cAMP, and associated
CAP activity, is influenced by glucose
• Glucose present  low cAMP
• Glucose absent  high cAMP

12.2 Regulation of Transcription in Bacteria
The lac Operon Is Also Under Positive Control
by an Activator Protein
• Glucose blocks activation of the lac operon; lactose relieves
repression of the lac operon

12.3 Regulation in Eukaryotes: Transcription Factors
Section 12.3 Learning
Outcomes
1. Explain the concept of
combinatorial control
2. Diagram a typical
eukaryotic promoter
3. Describe how RNA
polymerase and general
transcription factors initiate
transcription at the core
promoter
4. Discuss how activators,
coactivators, repressors,
and TFIID play a role in
gene regulation

12.3 Regulation in Eukaryotes: Transcription Factors
• Eukaryotic regulation of transcription involves some of the same
principles as prokaryotic regulation
• Activator and repressor proteins influence the ability of RNA
polymerase to initiate transcription; small effector molecules
may participate in regulation
• Eukaryotic regulation differs in many important ways
• Genes are almost always organized individually (not in operons)
• Regulation tends to be more intricate
• Most eukaryotic genes are
under combinatorial control,
where expression is regulated by
the combination of many factors

12.3 Regulation in Eukaryotes: Transcription Factors
Combinatorial control of transcription involves:
1. Activators – activator proteins stimulate RNA polymerase to
initiate transcription
2. Repressors – repressor proteins inhibit RNA polymerase from
initiating transcription
3. Modulation – small effector molecules, protein–protein
interactions, and covalent modifications can modulate activators
and repressors
4. Chromatin structure – activator proteins promote loosening up
of the region in the chromosome where a gene is located, making
it easier for RNA polymerase to transcribe the gene
5. DNA Methylation – usually inhibits transcription, either by
blocking an activator protein or by recruiting proteins that inhibit
transcription

12.3 Regulation in Eukaryotes: Transcription Factors
Eukaryotic Protein-Encoding Genes Have a Core
Promoter and Regulatory Elements
• Most promoters include a core promoter and regulatory elements
• The core promoter contains the TATA box and the transcription
start site
• The TATA box (5’–TATAAAA–3’) is about 25 bp upstream from the
transcription start site, where transcription actually begins
• The core promoter alone results in a low-level basal transcription

12.3 Regulation in Eukaryotes: Transcription Factors
Eukaryotic Protein-Encoding Genes Have a Core
Promoter and Regulatory Elements
• The regulatory elements (aka regulatory sequences) are recognized
by regulatory transcription factors
• There are 2 general types of regulatory elements: enhancers
and silencers; enhancers increase transcription and silencers
decrease transcription
• Regulatory
elements are often
near the core
promoter however,
they can be distant
(100,000 bp away)

12.3 Regulation in Eukaryotes: Transcription Factors
RNA Polymerase II and General Transcription Factors Are
Needed to Transcribe Protein-Encoding Genes
• RNA polymerase II transcribes genes that encode proteins
• RNA polymerase II requires 5 different general transcription factors
(GTFs) to initiate transcription; these proteins are sometimes called
basal transcription factors
• RNA polymerase II and the GTFs are assembled together at the
TATA box of the core promoter, forming the preinitiation complex

12.3 Regulation in Eukaryotes: Transcription Factors
Activators and Repressors May Influence the Function
of General Transcription Factors (GTFs)
• Activators are regulatory proteins
that bind to enhancer sequences;
repressors are regulatory proteins
that bind to silencer sequences
• Activators and repressors
commonly exert their regulation of
transcription through affecting the
function of GTFs
• In this example an activator and a
coactivator are involved
• TFIID binds the TATA box and is a
common target for activators and
repressors

12.4 Regulation in Eukaryotes: Chromatin Structure
Section 12.4 Learning
Outcomes
1. Describe the functions of
chromatin-remodeling
complexes
2. Describe nucleosome-free
regions and explain how
nucleosomes are altered
during gene transcription
3. Explain how DNA methylation
affects transcription
4. Describe how the formation of
facultative heterochromatin
can silence genes in a tissue-
specific manner

12.4 Regulation in Eukaryotes: Chromatin Structure
• DNA is associated with proteins to form chromatin
• Depending on the locations and arrangements of nucleosomes,
regions of DNA may or may not be accessible for transcription
• A region in a closed conformation is difficult or impossible to
transcribe; transcription requires changes in chromatin structure
• A region in an open conformation is accessible to GTFs and RNA
polymerase II and can therefore be transcribed

12.4 Regulation in Eukaryotes: Chromatin Structure
Transcription Is Controlled by Changes in
Chromatin Structure
• One way to change chromatin structure is
through chromatin-remodeling
complexes
• The complex is a group of proteins
that use energy from ATP hydrolysis
to drive a change in the locations
and/or compositions of nucleosomes
• Nucleosome locations can be changed,
histones can be evicted, or standard
histone proteins can be replaced with
variants
• These changes can potentially make the
DNA more or less accessible for
transcription  important for both
activation and repression of transcription

12.4 Regulation in Eukaryotes: Chromatin Structure
Histone Modifications Affect Gene Transcription
• The amino terminal tails of
histone proteins are subject to
several types of covalent
modifications
• ex: acetylation, methylation,
phosphorylation
• Modifications influence histone
function
• ex: acetylated histone
proteins do not bind as
tightly to DNA  promotes
transcription
• Modifications may directly influence interactions between DNA and
histone proteins and between adjacent nucleosomes

12.4 Regulation in Eukaryotes: Chromatin Structure
Eukaryotic Genes Are Flanked by
Nucleosome-Free Regions
• Many eukaryotic genes show a common pattern of nucleosome
organization: a nucleosome-free region (NFR) is found at the
beginning and end of the gene
• Although the NFR may be required for transcription, it alone is
not sufficient for transcription
• The +1 and -1 nucleosomes that flank the NFR with the core
promoter often contain histone variants that promote transcription

12.4 Regulation in Eukaryotes: Chromatin Structure
Transcriptional Activation Involves Changes in
Nucleosome Locations and Changes in Histones
• A key role of certain activators is to recruit chromatin-remodeling
complexes and histone-modifying enzymes to the promoter region
• A common sequence is
1. Activator binds enhancer in NFR
2. Chromatin-remodeling complex and histone-modifying
enzymes are recruited
3. The binding of GTFs and RNA polymerase II to the core
promoter is facilitated; the preinitiation complex forms
4. For transcription to occur, histones are evicted, partially
displaced, or destabilized so RNA polymerase II can pass

12.4 Regulation in Eukaryotes: Chromatin Structure
Transcriptional Activation Involves Changes in
Nucleosome Locations and Changes in Histones

12.4 Regulation in Eukaryotes: Chromatin Structure
DNA Methylation Inhibits Gene Transcription
• DNA methyltransferase is an enzyme that attaches methyl groups
(–CH3) to cytosine
• Methylation is common in some, but not all eukaryotes; in
mammals about 5% of DNA is methylated
• Methylation typically inhibits transcription, particularly when it is
near a promoter; CpG islands are clusters of CG bases that are
often near promoters and are sites of regulation via methylation
• unmethylated  active genes
• methylated  repressed genes
• Methylation can inhibit transcription
by preventing the binding of an
activator or by facilitating the binding
of proteins that inhibit transcription
Fig 11.15, Principles of Life, 2014 Sinauer Associates, Inc.

12.4 Regulation in Eukaryotes: Chromatin Structure
The Formation of Facultative Heterochromatin Is a
Way to Silence Genes in a Tissue-Specific Manner
• Regions of chromosomes can exist as highly compacted
heterochromatin or as less condensed euchromatin
• Regions of heterochromatin that differ among cell types are known
as facultative heterochromatin
• For example, a segment of DNA that is within facultative
heterochromatin in muscle cells may be packaged as
euchromatin in neurons
• The genes in this same segment of DNA would be silenced in
muscle but could be expressed in neurons

12.4 Regulation in Eukaryotes: Chromatin Structure
The Formation of Facultative Heterochromatin Is a
Way to Silence Genes in a Tissue-Specific Manner
• During embryonic development, certain regions of chromosomes
are targeted to become facultative heterochromatin
• This targeting may involve
specific types of histone
modifications and DNA
methylation of CpG islands
• Once formed, the pattern of
facultative heterochromatin
is maintained following cell
division, allowing specific
genes to be silenced in a
tissue-specific manner

12.5 Eukaryotic Regulation of RNA Splicing and Translation
Section 12.5 Learning
Outcomes
1. Outline the process of
alternative splicing, and
explain how it increases
protein diversity
2. Explain how RNA-binding
proteins regulate the
translation of specific
mRNAs, using the
regulation of iron
absorption in mammals as
an example

12.5 Eukaryotic Regulation of RNA Splicing and Translation
Alternative Splicing of Pre-mRNAs Increases
Protein Diversity
• Regulation of transcription is efficient however it requires a fair
amount of time to drive effects in cell function; faster regulation
can be achieved at the stages of pre-mRNA splicing and translation
• Alternative splicing forms multiple different polypeptides from a
pre-mRNA that has multiple introns and exons
• This form of gene regulation allows an organism to use the same
gene to make different proteins at different stages of development,
in different cell types, and/or in response to a change in
environmental conditions

12.5 Eukaryotic Regulation of RNA Splicing and Translation
Alternative Splicing Is More Prevalent in Complex
Eukaryotic Species
• Alternative splicing increases the proteome size without increasing
the total number of genes
• The frequency of alternative splicing tends to increase with more
biological complexity

12.5 Eukaryotic Regulation of RNA Splicing and Translation
The Prevention of Iron Toxicity in Mammals Involves
the Regulation of Translation
• Another way to regulate mRNAs involves RNA-binding proteins
that directly affect the initiation of translation
• Iron is a vital cofactor for many
enzymes however, it is toxic at
high levels
• The protein ferritin prevents
toxicity by storing excess iron
• The mRNA that encodes
ferritin is controlled by an RNA
binding protein known as iron
regulatory protein (IRP)
• Regulation at the level of
translation is faster than
transcriptional regulation

Chapter 12 Summary
12.1 Overview of gene regulation
• Bacteria regulate genes in response to changes in their environment
• Eukaryotic gene regulation produces different cell types in a single
organism
• Eukaryotic gene regulation enables multicellular organisms to
proceed through developmental stages
• Gene regulation occurs at different points in the process from DNA
to protein
12.2 Regulation of transcription in bacteria
• Transcriptional regulation involves regulatory transcription factors
and small effector molecules
• The lac operon contains genes that encode proteins involved in
lactose metabolism
• The lac operon is under negative control by a repressor protein
• The lac operon is also under positive control by an activator protein

Chapter 12 Summary
12.3 Regulation of transcription in eukaryotes: roles of transcription
factors
• Eukaryotic protein-encoding genes have a core promoter and
regulatory elements
• RNA polymerase II and general transcription factors are needed to
transcribe protein-encoding genes in eukaryotes
• Activators and repressors may influence the function of GTFs
12.4 Regulation of transcription in eukaryotes: changes in chromatin
structure and DNA methylation
• Transcription is controlled by changes in chromatin structure
• Histone modifications affect gene transcription
• Eukaryotic genes are flanked by nucleosome-free regions
• Transcriptional activation involves changes in nucleosome
locations and changes in histones
• DNA methylation inhibits gene transcription
• Formation of facultative heterochromatin is a way to silence genes
in a tissue-specific manner

Chapter 12 Summary
12.5 Regulation of RNA splicing and translation in eukaryotes
• Alternative splicing of pre-mRNAs increases protein diversity
• Alternative splicing is more prevalent in complex eukaryotic
species
• The prevention of iron toxicity in mammals involves the
regulation of translation