Transcript Gene7-21

Chapter 21
Regulation of
Transcription
21.1 Introduction
21.2 Response elements identify genes under common regulation
21.3 There are many types of DNA-binding domains
21.4 A zinc finger motif is a DNA-binding domain
21.5 Steroid receptors are transcription factors
21.6 Steroid receptors have zinc fingers
21.7 Binding to the response element is activated by ligand-binding
21.8 Steroid receptors recognize response elements by a combinatorial code
21.9 Homeodomains bind related targets in DNA
21.10 Helix-loop-helix proteins interact by combinatorial association
21.11 Leucine zippers are involved in dimer formation
21.12 Transcription initiation requires changes in chromatin structure
21.13 Chromatin remodeling is an active process
21.14 Activation of transcription requires changes in nucleosome organization at the promoter
21.15 Histone acetylation and deacetylation control chromatin activity
21.16 Polycomb and trithorax are antagonistic repressors and activators
21.17 An LCR may control a domain
21.18 Insulators block enhancer actions
21.19 Insulators can vary in strength
21.20 A domain has several types of elements
21.21 Gene expression is associated with demethylation
21.22 CpG islands are regulatory targets
21.1 Introduction
Activation of gene structure
Initiation of transcription
Processing the transcript
Transport to cytoplasm
Translation of mRNA
21.2 Response elements identify genes under
common regulation
Regulatory Agent Module
Consensus
Factor
Heat shock
HSE
CNNGAANNTCCNNG
HSTF
Glucocorticoid
GRE
TGGTACAAATGTTCT
Receptor
Phorbol ester
TRE
TGACTCA
AP1
Serum
SRE
CCATATTAGG
SRF
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
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.
21.3 There are many
types of DNA-binding
domains
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 DNAbinding domains
Figure 28.19 Oncogenes
that code for
transcription factors
have mutations that
inactivate transcription
(v-erbA and possibly vrel) or that activate
transcription (v-jun and
v-fos).
21.4 A zinc finger motif is a DNA-binding domain
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
Figure 21.4 Zinc
fingers may form
a-helices that
insert into the
major groove,
associated with bsheets on the other
side.
21.4 A zinc finger motif is a
DNA-binding domain
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
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
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
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
Figure 21.8 Receptors
for many steroid and
thyroid hormones have
a similar organization,
with an individual Nterminal region,
conserved DNAbinding region, and a
C-terminal hormonebinding region.
21.5 Steroid receptors have
several independent domains
Figure 21.8 Receptors
for many steroid and
thyroid hormones have
a similar organization,
with an individual Nterminal region,
conserved DNAbinding region, and a
C-terminal hormonebinding region.
21.5 Steroid receptors have
several independent domains
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
Figure 21.19
Coactivators
may have HAT
activities that
acetylate the
tails of
nucleosomal
histones.
21.5 Steroid receptors have
several independent domains
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
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.
21.6 Homeodomains bind
related targets in DNA
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
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
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 Nterminal arm lies in the
minor groove, and makes
additional contacts.
21.6 Homeodomains bind related targets in DNA
Figure 29.8 The
posterior pathway
has two branches,
responsible for
abdominal
development and
germ cell
formation.
21.7 Helix-loop-helix proteins interact by combinatorial association
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
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.
21.8 Leucine zippers are involved in dimer formation
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
Figure 20.19 An enhancer contains several structural motifs.
The histogram plots the effect of all mutations that reduce
enhancer function to <75% of wild type. Binding sites for
proteins are indicated below the histogram.
21.9 Chromatin remodeling is an active process
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
Figure 21.16 The preemptive 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
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
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
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.
21.10 Histone acetylation and deacetylation
control chromatin activity
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
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
Figure 21.19
Coactivators
may have
HAT activities
that acetylate
the tails of
nucleosomal
histones.
21.10 Histone acetylation
and deacetylation control
chromatin activity
Figure 21.20 A
repressor
complex contains
three components:
a DNA binding
subunit, a
corepressor, and a
histone
deacetylase.
21.11 Polycomb and trithorax are antagonistic
repressors and activators
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
Figure 19.45
Extension of
heterochromatin
inactivates genes. The
probability that a
gene will be
inactivated depends
on its distance from
the heterochromatin
region.
21.12 Long range regulation and
insulation of domains
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
Figure 4.1 Each of
the a-like and blike 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
Figure 4.1 Each of
the a-like and blike 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
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
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
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
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
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
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
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
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.
21.13 Gene expression is associated with demethylation
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
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
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
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
>10 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
Figure 21.20 A
repressor complex
contains three
components: a
DNA binding
subunit, a
corepressor, and a
histone
deacetylase.
Summary
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
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
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.