Regulation of Transcription

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Chapter 21

• Regulation of Transcription

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21.1 Introduction21.2 Response elements identify
genes under common regulation21.3 There are many
types of DNA-binding domains21.4 A zinc finger
motif is a DNA-binding domain21.5 Steroid
receptors are transcription factors21.6 Steroid
receptors have zinc fingers21.7 Binding to the
response element is activated by
ligand-binding21.8 Steroid receptors recognize
response elements by a combinatorial code21.9
Homeodomains bind related targets in DNA21.10
Helix-loop-helix proteins interact by
combinatorial association21.11 Leucine zippers
are involved in dimer formation21.12
Transcription initiation requires changes in
chromatin structure21.13 Chromatin remodeling is
an active process21.14 Activation of
transcription requires changes in nucleosome
organization at the promoter21.15 Histone
acetylation and deacetylation control chromatin
activity21.16 Polycomb and trithorax are
antagonistic repressors and activators21.17 An
LCR may control a domain21.18 Insulators block
enhancer actions21.19 Insulators can vary in
strength21.20 A domain has several types of
elements21.21 Gene expression is associated with
demethylation 21.22 CpG islands are regulatory
targets
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Activation of gene structureInitiation of
transcriptionProcessing the transcriptTransport
to cytoplasmTranslation of mRNA
21.1 Introduction
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Table 21.1 Incucible transcription factors bind
to response elements that identify groups of
promoters or enhancers subject to coordinate
control.
21.2 Response elements identify genes under
common regulation
5
Figure 21.1 The regulatory region of a human
metallothionein gene contains regulator elements
in both its promoter and enhancer. The promoter
has elements for metal induction an enhancer has
an element for response to glucocorticoid.
Promoter elements are shown above the map, and
proteins that bind them are indicated below.
21.2 Response elements identify genes under
common regulation
6
Figure 21.2 The activity of a regulatory
transcription factor may be controlled by
synthesis of protein, covalent modification of
protein, ligand binding, or binding of inhibitors
that sequester the protein or affect its ability
to bind to DNA.
21.3 There are many types of DNA-binding domains
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Figure 28.19 Oncogenes that code for
transcription factors have mutations that
inactivate transcription (v-erbA and possibly
v-rel) or that activate transcription (v-jun and
v-fos).
21.3 There are many types of DNA-binding domains
8
Figure 21.3 Transcription factor SP1 has a
series of three zinc fingers, each with a
characteristic pattern of cysteine and histidine
residues that constitute the zinc-binding site.
21.4 A zinc finger motif is a DNA-binding domain
9
Figure 21.4 Zinc fingers may form a-helices that
insert into the major groove, associated with
b-sheets on the other side.
21.4 A zinc finger motif is a DNA-binding domain
10
Figure 21.5 The first finger of a steroid
receptor controls specificity of DNA-binding
(positions shown in red) the second finger
controls specificity of dimerization (positions
shown in blue). The expanded view of the first
finger shows that discrimination between GRE and
ERE target sequences rests on two amino acids at
the base.
21.4 A zinc finger motif is a DNA-binding domain
11
Receptor is a transmembrane protein, located in
the plasma membrane, that binds a ligand in a
domain on the extracellular side, and as a result
has a change in activity of the cytoplasmic
domain. (The same term is sometimes used also for
the steroid receptors, which are transcription
factors that are activated by binding ligands
that are steroids or other small molecules.)
21.5 Steroid receptors have several independent
domains
12
Figure 21.6 Several types of hydrophobic small
molecules activate transcription factors.
Corticoids and steroid sex hormones are
synthesized from cholesterol, vitamin D is a
steroid, thyroid hormones are synthesized from
tyrosine, and retinoic acid is synthesized from
isoprene (in fish liver).
21.5 Steroid receptors have several independent
domains
13
Figure 21.7 Glucocorticoids regulate gene
transcription by causing their receptor to bind
to an enhancer whose action is needed for
promoter function.
21.5 Steroid receptors have several independent
domains
14
Figure 21.8 Receptors for many steroid and
thyroid hormones have a similar organization,
with an individual N-terminal region, conserved
DNA-binding region, and a C-terminal
hormone-binding region.
21.5 Steroid receptors have several independent
domains
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Figure 21.8 Receptors for many steroid and
thyroid hormones have a similar organization,
with an individual N-terminal region, conserved
DNA-binding region, and a C-terminal
hormone-binding region.
21.5 Steroid receptors have several independent
domains
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Figure 21.5 The first finger of a steroid
receptor controls specificity of DNA-binding
(positions shown in red) the second finger
controls specificity of dimerization (positions
shown in blue). The expanded view of the first
finger shows that discrimination between GRE and
ERE target sequences rests on two amino acids at
the base.
21.5 Steroid receptors have several independent
domains
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Figure 21.19 Coactivators may have HAT activities
that acetylate the tails of nucleosomal histones.
21.5 Steroid receptors have several independent
domains
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Figure 21.20 A repressor complex contains three
components a DNA binding subunit, a corepressor,
and a histone deacetylase.
21.5 Steroid receptors have several independent
domains
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Figure 21.9 TR and RAR bind the SMRT corepressor
in the absence of ligand. The promoter is not
expressed. When SMRT is displaced by binding of
ligand, the receptor binds a coactivator complex.
This leads to activation of transcription by the
basal apparatus.
21.5 Steroid receptors have several independent
domains
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Figure 21.10 The homeodomain may be the sole
DNA-binding motif in a transcriptional regulator
or may be combined with other motifs. It
represents a discrete (60 residue) part of the
protein.
21.6 Homeodomains bind related targets in DNA
21
Figure 21.11 The homeodomain of the Antennapedia
gene represents the major group of genes
containing homeoboxes in Drosophila engrailed
(en) represents another type of homeotic gene
and the mammalian factor Oct-2 represents a
distantly related group of transcription factors.
The homeodomain is conventionally numbered from 1
to 60. It starts with the N-terminal arm, and the
three helical regions occupy residues
10-22,28-38, and 42-58.
21.6 Homeodomains bind related targets in DNA
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Figure 21.12 Helix 3 of the homeodomain binds in
the major groove of DNA, with helices 1 and 2
lying outside the double helix. Helix 3 contacts
both the phosphate backbone and specific bases.
The N-terminal arm lies in the minor groove, and
makes additional contacts.
21.6 Homeodomains bind related targets in DNA
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Figure 29.8 The posterior pathway has two
branches, responsible for abdominal development
and germ cell formation.
21.6 Homeodomains bind related targets in DNA
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Figure 21.13 All HLH proteins have regions
corresponding to helix 1 and helix 2, separated
by a loop of 10-24 residues. Basic HLH proteins
have a region with conserved positive charges
immediately adjacent to helix 1.
21.7 Helix-loop-helix proteins interact by
combinatorial association
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Figure 21.14 An HLH dimer in which both subunits
are of the bHLH type can bind DNA, but a dimer in
which one subunit lacks the basic region cannot
bind DNA.
21.7 Helix-loop-helix proteins interact by
combinatorial association
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Figure 21.15 The basic regions of the bZIP motif
are held together by the dimerization at the
adjacent zipper region when the hydrophobic faces
of two leucine zippers interact in parallel
orientation.
21.8 Leucine zippers are involved in dimer
formation
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Figure 20.19 An enhancer contains several
structural motifs. The histogram plots the effect
of all mutations that reduce enhancer function to
lt75 of wild type. Binding sites for proteins are
indicated below the histogram.
21.8 Leucine zippers are involved in dimer
formation
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Chromatin remodeling describes the
energy-dependent displacement or reorganization
of nucleosomes that occurs in conjunction with
activation of genes for transcription.
21.9 Chromatin remodeling is an active process
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Figure 21.16 The pre-emptive model for
transcription of chromatin proposes that if
nucleosomes form at a promoter, transcription
factors (and RNA polymerase) cannot bind. If
transcription factors (and RNA polymerase) bind
to the promoter to establish a stable complex for
initiation, histones are excluded.
21.9 Chromatin remodeling is an active process
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Figure 21.17 The dynamic model for transcription
of chromatin relies upon factors that can use
energy provided by hydrolysis of ATP to displace
nucleosomes from specific DNA sequences.
21.9 Chromatin remodeling is an active process
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Figure 21.18 Hormone receptor and NF1 cannot bind
simultaneously to the MMTV promoter in the form
of linear DNA, but can bind when the DNA is
presented on a nucleosomal surface.
21.9 Chromatin remodeling is an active process
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Figure 21.18 Hormone receptor and NF1 cannot bind
simultaneously to the MMTV promoter in the form
of linear DNA, but can bind when the DNA is
presented on a nucleosomal surface.
21.9 Chromatin remodeling is an active process
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HAT (histone acetyltransferase) enzymes modify
histones by addition of acetyl groups some
transcriptional coactivators have HAT
activity.HDAC (histone deacetyltransferase)
enzymes remove acetyl groups from histones they
may be associated with repressors of
transcription.
21.10 Histone acetylation and deacetylation
control chromatin activity
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Figure 20.26 An upstream transcription factor may
bind a coactivator that contacts the basal
apparatus.
21.10 Histone acetylation and deacetylation
control chromatin activity
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Figure 21.19 Coactivators may have HAT activities
that acetylate the tails of nucleosomal histones.
21.10 Histone acetylation and deacetylation
control chromatin activity
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Figure 21.20 A repressor complex contains three
components a DNA binding subunit, a corepressor,
and a histone deacetylase.
21.10 Histone acetylation and deacetylation
control chromatin activity
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Figure 21.21 Pc-G proteins do not initiate
repression, but are responsible for maintaining
it.
21.11 Polycomb and trithorax are antagonistic
repressors and activators
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Figure 19.45 Extension of heterochromatin
inactivates genes. The probability that a gene
will be inactivated depends on its distance from
the heterochromatin region.
21.11 Polycomb and trithorax are antagonistic
repressors and activators
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Domain of a chromosome may refer either to a
discrete structural entity defined as a region
within which supercoiling is independent of other
domains or to an extensive region including an
expressed gene that has heightened sensitivity to
degradation by the enzyme DNAase I.MAR (matrix
attachment site also known as SAR for scaffold
attachment site) is a region of DNA that attaches
to the nuclear matrix.
21.12 Long range regulation and insulation of
domains
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Figure 4.1 Each of the a-like and b-like globin
gene families is organized into a single cluster
that includes functional genes and pseudogenes
(y).
21.12 Long range regulation and insulation of
domains
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Figure 4.1 Each of the a-like and b-like globin
gene families is organized into a single cluster
that includes functional genes and pseudogenes
(y).
21.12 Long range regulation and insulation of
domains
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Figure 21.22 A globin domain is marked by
hypersensitive sites at either end. The group of
sites at the 5? side constitutes the LCR and is
essential for the function of all genes in the
cluster.
21.12 Long range regulation and insulation of
domains
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Figure 19.42 Sensitivity to DNAase I can be
measured by determining the rate of disappearance
of the material hybridizing with a particular
probe.
21.12 Long range regulation and insulation of
domains
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Figure 21.23 Specialized chromatin structures
that include hypersensitive sites mark the ends
of a domain in the D. melanogaster genome and
insulate genes between them from the effects of
surrounding sequences.
21.12 Long range regulation and insulation of
domains
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Figure 21.24 A protein that binds to the
insulator scs? is localized at interbands in
Drosophila polytene chromosomes. Red staining
identifies the DNA (the bands) on both the upper
and lower samples green staining identifies
BEAF32 (often at interbands) on the upper sample.
Yellow shows coincidence of the two labels. Some
of the more prominent stained interbands are
marked by white lines. Photograph kindly provided
by Uli Laemmli.
21.12 Long range regulation and insulation of
domains
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Figure 21.25 The insulator of the gypsy
transposon blocks the action of an enhancer when
it is placed between the enhancer and the
promoter.
21.12 Long range regulation and insulation of
domains
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Figure 29.32 The homeotic genes of the ANT-C
complex confer identity on the most anterior
segments of the fly. The genes vary in size, and
are interspersed with other genes. The antp gene
is very large and has alternative forms of
expression.
21.12 Long range regulation and insulation of
domains
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Figure 21.26 Fab-7 is a boundary element that is
necessary for the independence of regulatory
elements iab-6 and iab-7.
21.12 Long range regulation and insulation of
domains
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Figure 21.27 Domains may possess three types of
sites insulators to prevent effects from
spreading between domains MARs to attach the
domain to the nuclear matrix and LCRs that are
required for initiation of transcription.
21.12 Long range regulation and insulation of
domains
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Figure 21.28 The restriction enzyme MspI cleaves
all CCGG sequences whether or not they are
methylated at the second C, but HpaII cleaves
only nonmethylated CCGG tetramers.
21.13 Gene expression is associated with
demethylation
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Figure 21.29 The results of MspI and HpaII
cleavage are compared by gel electrophoresis of
the fragments.
21.13 Gene expression is associated with
demethylation
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Figure 13.30 Replication of methylated DNA gives
hemimethylated DNA, which maintains its state at
GATC sites until the Dam methylase restores the
fully methylated condition.
21.13 Gene expression is associated with
demethylation
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Figure 21.30 The typical density of CpG doublets
in mammalian DNA is 1/100 bp, as seen for a
g-globin gene. In a CpG-rich island, the density
is increased to gt10 doublets/100 bp. The island
in the APRT gene starts 100 bp upstream of the
promoter and extends 400 bp into the gene. Each
vertical line represents a CpG doublet.
21.13 Gene expression is associated with
demethylation
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Figure 21.20 A repressor complex contains three
components a DNA binding subunit, a corepressor,
and a histone deacetylase.
21.13 Gene expression is associated with
demethylation
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1. Some regulatory promoter elements are present
in many genes and are recognized by ubiquitous
factors others are present in a few genes and
are recognized by tissue-specific factors. 2.
Several groups of transcription factors have been
identified by sequence homologies. 3. Another
motif involved in DNA-binding is the zinc finger,
which is found in proteins that bind DNA or RNA
(or sometimes both). 4. Steroid receptors were
the first members identified of a group of
transcription factors in which the protein is
activated by binding a small hydrophobic
hormone.5. The leucine zipper contains a stretch
of amino acids rich in leucine that are involved
in dimerization of transcription factors.
Summary
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6. HLH (helix-loop-helix) proteins have
amphipathic helices that are responsible for
dimerization, adjacent to basic regions that bind
to DNA.7. Many transcription factors function as
dimers, and it is common for there to be multiple
members of a family that form homodimers and
heterodimers. 8. The existence of a
preinitiation complex signals that the gene is in
an "active" state, ready to be transcribed.9.
The variety of situations in which hypersensitive
sites occur suggests that their existence
reflects a general principle. 10. Genes whose
control regions are organized in nucleosomes
usually are not expressed.
Summary
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11. Acetylation of histones occurs at both
replication and transcription and could be
necessary to form a less compact chromatin
structure. 12. Active chromatin and inactive
chromatin are not in equilibrium. 13. A group of
hypersensitive sites upstream of the cluster of
-globin genes forms a locus control region (LCR)
that is required for expression of all of the
genes in the domain. 14. CpG islands contain
concentrations of CpG doublets and often surround
the promoters of constitutively expressed genes,
although they are also found at the promoters of
regulated genes. 15. The formation of
heterochromatin occurs by proteins that bind to
specific chromosomal regions (such as telomeres)
and that interact with histones.
Summary