Differential Gene Expression

Differential gene transcription

• Different cell types make different sets of proteins, even though
their genomes are identical. Each cell uses only a small subset of
the genes in their genomes.
• Different cell types use different subsets of these genes.
• Red blood cells make globins, lens cells make crystallins,
melanocytes make melanin, and endocrine glands make their
specific hormones.
• The regulation of gene expression can be done at several levels:
• Differential gene transcription, regulating which of the nuclear genes are
transcribed into RNA
• Selective nuclear RNA processing, regulating which of the transcribed
RNAs (or which parts of such a nuclear RNA) enter into the cytoplasm to
become messenger RNAs
• Selective messenger RNA translation, regulating which of the mRNAs in the
cytoplasm become translated into proteins
• Differential protein modification, regulating which proteins are allowed to
remain or function in the cell
Anatomy of the gene: introns and
exons
Eukaryotic genes vs prokaryotic genes
• Eukaryotic genes are contained
within a complex of DNA and
protein called chromatin.
• Eukaryotic genes are not co-linear
with their peptide products. Rather,
the single nucleic acid strand of
eukaryotic mRNA comes from
noncontiguous regions on the
chromosome.
• Exons are regions of DNA coding
for a protein
• Introns are intervening sequences
that do not code for proteins
Structure of the gene
• Promoter region - responsible for the binding of RNA polymerase and for the
subsequent initiation of transcription.

• Transcription initiation site - often called the cap sequence because it

represents the 5´ end of the RNA, which will receive a "cap“ of modified
nucleotides soon after it is transcribed; the specific cap sequence varies among
genes.
Structure of the gene
• Translation initiation site (ATG; AUG in the mRNA) - located after the
transcription initiation site; the distance differs greatly among different genes.
The intervening sequence of 50 base pairs between the initiation points of
transcription and translation is the 5´ untranslated region, often called the 5´
UTR or leader sequence. The 5´ UTR can determine the rate at which
translation is initiated.
Structure of the gene
• First exon
• Intron, the structure of which is important in enabling the RNA to be
processed into messenger RNA and exit from the nucleus.
• Translation termination codon (TAA; UAA in the mRNA) - the ribosome
dissociates at this codon, and the protein is released.
• 3´ untranslated region (3´ UTR) - although transcribed, is not translated
into protein. This region includes the sequence AATAAA, which is
needed for polyadenylation: the placement of a "tail" of some 200 to
300 adenylate residues on the RNA transcript.
• confers stability on the mRNA
• allows the mRNA to exit the nucleus
• permits the mRNA to be translated into protein.
• The poly(A) tail is inserted into the RNA about 20 bases downstream of
the AAUAAA sequence. Transcription continues beyond the AATAAA site
for about 1000 nucleotides before being terminated.
Structure of the gene
• A cap consisting of methylated guanosine is placed on the 5´ end of the RNA in
opposite polarity to the RNA itself. The 5´ cap is necessary for the binding of
mRNA to the ribosome and for subsequent translation

• The 3´ end is usually modified in the nucleus by the addition of a poly(A) tail.
These adenylate residues are put together enzymatically and are added to the
transcript; they are not part of the gene sequence.
• Both the 5´ and 3´ modifications may protect the RNA from exonucleases that
would otherwise digest the mRNA; the modifications thus stabilize the message
and its precursor.
Regulatory sequences
• In addition to the protein-encoding region of the gene, there are regulatory
sequences that can be on either end of the gene (or even within it). These
sequences are necessary for controlling where and when a particular gene is
transcribed.
• Promoters - the sites where RNA polymerase binds to the DNA to initiate
transcription.
• typically located immediately upstream from the site where the RNA polymerase
initiates transcription
• most contain the sequence TATA called the TATA box, where RNA polymerase will
be bound (usually about 30 bp upstream from the site where the first base is
transcribed.
Regulatory sequences
• Eukaryotic RNA polymerases will not bind to this naked DNA sequence; they
require additional protein factors to bind efficiently to the promoter. At least
six nuclear proteins called basal transcription factors have been shown to be
necessary for the proper initiation of transcription by RNA polymerase II
• There is also a set of transcription factors called TBP-associated factors, or
TAFs which can stabilize the TBP. These DNA sequences are near, usually
upstream from the TATA sequence. These TAFs need not be in every cell.
• Cell-specific transcription factors can also activate the gene by stabilizing the
transcription initiation complex either by binding to the TAFs, by binding
directly to other factors such as TFIIB, or by destabilizing nucleosomes.
• Enhancer - a DNA sequence that can activate the utilization of a promoter,
controlling the efficiency and rate of transcription from that particular
promoter.
• Enhancers can activate only cis-linked promoters (i.e., promoters on the
same chromosome), but they can do so at great distances
• Enhancers do not need to be on the 5´ (upstream) side of the gene. They
can also be at the 3´ end, in the introns, or even on the complementary DNA
strand
• Like promoters, enhancers function by binding specific regulatory proteins
called transcription factors.
• Enhancers can regulate the temporal and tissue-specific expression of any
differentially regulated gene, but different types of genes normally have
different enhancers.
• By taking an enhancer from one gene and fusing it to another gene, it has
been shown that enhancers can direct the expression of any gene sequence.
• For example, if the gene for green fluorescent protein (a reporter protein) is
placed on the enhancer of genes encoding the crystallin proteins of the eye
lens, GFP expression is seen solely in the lens
Enhancers are critical in the regulation of normal development
• Most genes require enhancers for their transcription.
• Enhancers are the major determinant of differential transcription in space
(cell type) and time.
• The ability of an enhancer to function while far from the promoter means that
there can be multiple signals to determine whether a given gene is
transcribed. A given gene can have several enhancer sites linked to it, and
each enhancer can be bound by more than one transcription factor.
• The interaction between the proteins bound to the enhancer sites and the
transcription initiation complex assembled at the promoter is thought to
regulate transcription.
• Enhancers are modular. There are various DNA elements that regulate
temporal and spatial gene expression, and these can be mixed and matched.
It is the combination of transcription factors that causes particular genes to
be transcribed.
• A gene can have several enhancer elements, each turning it on in a different
set of cells
• Enhancers can also inhibit transcription. In some cases, the same transcription
factors that activate the transcription of one gene, repress the transcription of
other genes. These "negative enhancers " are also called silencers.
Transcription factors
• Transcription factors are proteins that bind to enhancer or promoter regions
and interact to activate or repress the transcription of a particular gene.
• Most transcription factors can bind to specific DNA sequences. These proteins
can be grouped together in families based on similarities in structure
• The transcription factors within a family share a common framework structure
in their DNA-binding sites, and slight differences in the amino acids at the
binding site can alter the sequence of the DNA to which the factor binds.
• Transcription factors have three major domains:
• a DNA-binding domain that recognizes a particular DNA sequence.
• a trans-activating domain that activates or suppresses the transcription of the
gene whose promoter or enhancer it has bound. Usually, this trans-activating
domain enables the transcription factor to interact with proteins involved in
binding RNA polymerase (such as TFIIB or TFIIE)
• a protein-protein interaction domain that allows the transcription factor's activity
to be modulated by TAFs or other transcription factors.
Silencers
• Some sequences called silencers act specifically to block transcription
• Silencer domains are useful in restricting the transcription of a particular gene
to a particular group of cells or for regulating the timing of the gene's
expression.
• For example, the fetal mouse liver makes serum albumin, but only after a certain
stage of gut development.
• At first, the endodermal cells that will
form the liver do not transcribe this
albumin gene.
• When the endodermal tube contacts
the cardiac mesoderm (which is in the
process of forming a heart),
the heart precursors are able to
instruct the endodermal tube
to begin forming the liver and
to start transcribing liver-specific genes
Locus control regions
• There are some regions of DNA called locus control regions (LCRs), which
function as "super-enhancers."
• LCRs establish an "open“ chromatin configuration, inhibiting the normal
repression of transcription over an area spanning several genes.
• The mechanism by which the LCR opens up the chromatin is not yet known.
• One of the best-studied LCRs is that regulating the tissue-specific expression
of the β-globin family of genes in humans, mice, and chicks where the
embryonic or fetal hemoglobin differs from that found in adult red blood cells
Mechanisms for control of transcription
DNA methylation and gene activity
• In 1948, R. D. Hotchkiss discovered a "fifth base" in DNA, 5- methylcytosine
which in vertebrates, is made enzymatically after DNA is replicated, at which
time about 5% of the cytosines in mammalian DNA are converted to 5-
methylcytosine. This conversion can occur only when the cytosine residue is
followed by a guanosine.
Mechanisms for control of transcription
• DNA methylation - the promoters of inactive genes become methylated at
certain cytosine residues, and the resulting methylcytosine stabilizes
nucleosomes and prevents transcription factors from binding.
• Recent studies have shown that the degree to which the cytosines of a gene
are methylated can control the level of the gene's transcription.
• Cytosine methylation appears to be a major mechanism of transcriptional
regulation in vertebrates where the presence of methylated cytosines in the
promoter of a gene correlates with the repression of transcription from that
gene. Drosophila, nematodes, and most invertebrates do not methylate DNA.
DNA methylation and gene activity
• In developing human and chick red blood cells, the DNA of the globin
promoters is almost completely unmethylated, whereas the same promoters
are highly methylated in cells that do not produce globin.
• The methylation pattern changes during development. The cells that produce
hemoglobin in the human embryo have unmethylated promoters for the
genes encoding the -globins of embryonic hemoglobin.
• These promoters become methylated in the fetal tissue. Similarly, when the
fetal globin gives way to adult globin, the -globin gene promoters become
methylated.
• The correlation between methylated cytosines and transcriptional repression
has been confirmed experimentally.
Genome imprinting
• It is assumed that the genes one inherits from one's father and mother are
equivalent.
• In certain mutations of mice and humans, a severe or lethal condition arises if
the mutant gene is derived from one parent, but that same mutant gene has
no deleterious effects if inherited from the other parent.
Genome imprinting
• For instance, in mice, the gene for Igf-2 on chromosome 7 is active in early
embryos only on the chromosome transmitted from the father.
• Conversely, the gene for Igf-2r that binds Igf-2 located on chromosome 17, is
active only in the chromosome transmitted from the mother.
• A mouse pup that inherits a deletion of the Igf-2r gene from its father is normal,
but if the same deletion is inherited from the mother, the fetus experiences a
30% increase in growth and dies late in gestation.
Genome imprinting
• In humans, the loss of a segment of the long arm of chromosome 15 results in
different phenotypes, depending on whether the loss is in the male- or the female-
derived chromosome.
• If the chromosome with the defective or missing segment comes from the father,
the child is born with Prader-Willi syndrome, a disease associated with mild
mental retardation, obesity, small gonads, and short stature.
• If the defective or missing segment comes from the mother, the child has
Angelman syndrome, characterized by severe mental retardation, seizures, lack of
speech, and inappropriate laughter.
Genome imprinting
• These differences involve methylation.
• In the primordial germ cells that give rise to the sperm and egg, all methylation
differences are wiped out. The DNA is almost entirely unmethylated.
• However, as the germ cells develop into sperm or eggs, their genes undergo
extensive methylation.
• The pattern of methylation on a given gene can differ between egg and sperm.
These gene-specific methylation differences can be seen in the chromosomes of
embryonic cells.
Transcriptional regulation of an entire chromosome
Dosage compensation
• Females have XX and males have XY chromosomes, yet, male and female cells
contain @ equal amounts of X chromosome-encoded gene products.
• This equalization is called dosage compensation. The transcription rates of the
X chromosomes are altered so that male and female cells transcribe the same
amount of RNAs from their X chromosomes.
• In Drosophila, both X chromosomes in the female are active, but there is
increased transcription from the male's X chromosome, so that the single X
chromosome of male cells produces as much product as the two X chromosomes
in female cells. This is accomplished by the binding of particular transcription
factors to hundreds of sites along the male X chromosome.
• In mammals, X chromosome dosage compensation occurs through the
inactivation of one X chromosome in each female cell. Thus, each mammalian
somatic cell, whether male or female, has only one functioning X chromosome.
This phenomenon is called X chromosome inactivation.
Transcriptional regulation of an entire chromosome
• X chromosome inactivation must occur early in development.
• Using a mutated X chromosome that would not inactivate, Tagaki and Abe (1990)
showed that the expression of two X chromosomes per cell in mouse embryos
leads to ectodermal cell death and the absence of mesoderm formation,
eventually causing embryonic death at day 10 of gestation.
• The early inactivation of one X chromosome per cell has important phenotypic
consequences.
Transcriptional regulation of
an entire chromosome
• One of the earliest analyses of X
chromosome inactivation was done
by Mary Lyon (1961), who observed
coat color patterns in mice.
• If a mouse is heterozygous for an
autosomal gene controlling hair
pigmentation, then it resembles
one of its two parents, or has a
color intermediate between the
two. In either case, the mouse is a
single color.
• But if a female mouse is
heterozygous for a pigmentation
gene on the X chromosome, a
different result is seen - patches of
one parental color alternate with
patches of the other parental color.
Chromosome inactivation
• Lyon proposed the following hypothesis to account for these results:
• Very early in the development of female mammals, both X chromosomes are
active.
• As development proceeds, one X chromosome is turned off in each cell.
• This inactivation is random. In some cells, the paternally derived X chromosome is
inactivated; in other cells, the maternally derived X chromosome is shut off.
• This process is irreversible. Once an X chromosome has been inactivated, the
same X chromosome is inactivated in all that cell's progeny. Since X inactivation
happens relatively early in development, an entire region of cells derived from a
single cell may all have the same X chromosome inactivated. Thus, all tissues in
female mammals are mosaics of two cell types.
Exceptions to the general rules
• First, X chromosome inactivation holds true only for somatic cells, not germ
cells. In female germ cells, the inactive X chromosome is reactivated shortly
before the cells enter meiosis. Thus, in early oocytes, both X chromosomes
are unmethylated (and active). In each generation, X chromosome
inactivation has to be established anew.
• Second, there are some exceptions to the rule of randomness in the
inactivation pattern. For instance, the first X chromosome inactivation in the
mouse is seen in the fetal portion of the placenta, where the paternally
derived X chromosome is specifically inactivated (Tagaki 1974).
• Third, X chromosome inactivation does not extend to every gene on the
human X chromosome. There are a few genes (such as that encoding steroid
sulfatase) on both arms of the X chromosome that "escape" X inactivation
(Brown et al. 1997).
Mechanism of X chromosome inactivation
Initiation of X chromosome inactivation by the Xist gene
• In 1991, Brown and colleagues found an RNA transcript that was made solely
from the inactive X chromosome of humans. This transcript, XIST, does not
encode a protein but stays within the nucleus and interacts with the inactive X
chromatin, forming an XIST-Barr body complex.
• In the mouse, the transcript of the Xist gene is seen to coat the inactive X
chromosome.
• The Xist gene is an excellent candidate for the initiator of X inactivation.
• The transcripts from the Xist gene are seen in mouse embryos prior to X
chromosome inactivation, which would be expected if this gene plays a role in
initiating inactivation.
• Knocking out one Xist locus in an XX cell prevents X inactivation from occurring on
that particular chromosome.
• The transfer of a 450-kilobase segment containing the mouse Xist gene into an
autosome of male embryonic stem cells causes the random inactivation of either
that autosome or the endogenous X chromosome The autosome is "counted" as
an X chromosome.
Mechanism of X chromosome
inactivation
Initiation of X chromosome inactivation
by the Xist gene
• Xist appears to be involved in
"choosing“ which X chromosome is
inactivated. Female mice
heterozygous for a deletion of a
particular region of the Xist gene will
preferentially inactivate the wild-
type chromosome. Xist expression is
needed only for the initiation of X
chromosome inactivation; once
inactivation occurs, Xist transcription
is dispensible.
• It is still not known what Xist RNA
does to inactivate the chromosome.
• When the cells begin to
differentiate, the Xist RNA is
stabilized on one of the two X
chromosomes. Xist RNA appears to
be critical in the counting, selection,
and intrachromosomal spreading of
X chromosome inactivation.
Mechanism of X chromosome inactivation
Maintaining X chromosome inactivation
• Once Xist initiates the inactivation of an X chromosome, the silencing of that
chromosome is maintained in at least two ways.
• The first involves methylation. The Xist locus on the active X chromosome
becomes methylated, while the active Xist gene (on the inactive X
chromosome) remains unmethylated
• Conversely, the promoter regions of numerous genes are methylated on the
inactive X chromosome and unmethylated on the active X chromosome (Wolf
et al. 1984; Keith et al. 1986; Migeon et al. 1991).
• Unknowns:
• the mechanisms by which the Xist transcript regulates the state of the
chromatin and by which the spreading of inactivation occurs
• how Xist transcription is linked to DNA methylation
• how the choice between the two X chromosomes is originally made
• how the Xist RNA is transcribed from a region surrounded by inactivated genes
Differential RNA processing
The regulation of gene expression is not confined to the differential
transcription of DNA. Even if a particular RNA transcript is synthesized,
there is no guarantee that it will create a functional protein in the cell. The
RNA must be:
• processed into a messenger RNA by the removal of introns
• translocated from the nucleus to the cytoplasm,
• translated by the protein-synthesizing apparatus.
• In some cases, the synthesized protein is not in its mature form and
must be post-translationally modified to become active.
• During development, regulation can occur at any of these steps.
• The essence of differentiation is the production of different sets of
proteins in different types of cells.
• In bacteria, differential gene expression can be effected at the levels
of transcription, translation, and protein modification.
• In eukaryotes, however, another possible level of regulation include
the control at the level of RNA processing and transport.
Differential RNA processing
There are two major ways in which differential RNA processing can
regulate development.
• "censoring" of which nuclear transcripts are processed into cytoplasmic
messages where, different cells can select different nuclear transcripts
to be processed and sent to the cytoplasm as messenger RNA. The same
pool of nuclear transcripts can thereby give rise to different populations
of cytoplasmic mRNAs in different cell types.
• The second mode of differential RNA processing is the splicing of the
mRNA precursors into messages for different proteins by using different
combinations of potential exons. If an mRNA precursor had five
potential exons, one cell might use exons 1, 2, 4, and 5; a different cell
might utilize exons 1, 2, and 3; and yet another cell type might use yet
another combination.
• Thus, one gene can create a family of related proteins.
Control of early development by nuclear RNA selection
• In the late 1970s, numerous investigators found that mRNA was not the
primary transcript from the genes.
• The genes transcribed nuclear RNA (nRNA), sometimes called heterogeneous
nuclear RNA (hnRNA) or pre-messenger RNA (pre-mRNA) that contains introns
that get spliced out during the passage from nucleus to cytoplasm.
• It was first thought that whatever RNA was transcribed in the nucleus was
processed into cytoplasmic mRNA, but studies of sea urchins showed that
different cell types could be transcribing the same type of nuclear RNA, but
processing different subsets of nRNAs into mRNA in different types of cells
• Wold and her colleagues showed that sequences present in sea urchin blastula
messenger RNA, but absent in gastrula and adult tissue mRNA, were present in
the nuclear RNA of the gastrula and adult tissues.
• More genes are transcribed in the nucleus than those that become mRNAs in
the cytoplasm.
• Gagnon and his colleagues examined the transcripts of the sea urchin CyIIIa
genes that encode calcium-binding and actin proteins that are expressed only
in a particular part of the ectoderm of the sea urchin larva.
• Using probes that bound to an exon and to an intron, they found that these
genes were being transcribed not only in the ectodermal cells, but also in the
mesoderm and endoderm.
• The concentration of introns was the same in both the gastrula ectoderm and
in the mesoderm/endoderm samples, suggesting that this gene was being
transcribed at the same rate in the nuclei of all cell types, but was made into
cytoplasmic mRNA only in ectodermal cells.
• The unprocessed nRNA for CyIIIa is degraded while still in the nuclei of the
endodermal and mesodermal cells.
Control of gene expression at the level of translation
Once the RNA has reached the cytoplasm, there is still no guarantee that it will be
translated. The control of gene expression at the level of translation can occur by
many means:
Differential mRNA longevity
• The longer an mRNA persists, the more protein can be translated from it.
• If a message with a relatively short half-life were selectively stabilized in certain
cells at certain times, it would make large amounts of its particular protein only at
those times and places.
• The stability of a message is often dependent upon the length of its poly(A) tail.
This, in turn, appears to depend upon sequences in the 3´ untranslated region.
Certain 3´ UTR sequences allow longer poly(A) tails than others.
• If these regions are experimentally traded, the half-lives of the resulting mRNAs
will be altered: usually long-lived messages will decay rapidly, while normally
short-lived mRNAs will remain around longer
• In some instances, messenger RNAs can be selectively stabilized at specific times
in specific cells.
• For example, the mRNA for casein, the major
protein of milk, has a half-life of 1.1 hours in
rat mammary gland tissue. However, during
periods of lactation, the presence of the
hormone prolactin increases this half-life
to 28.5 hours.
Selective inhibition of mRNA translation
Some of the most remarkable cases of translational regulation of gene
expression occur in the oocyte.
• The oocyte often makes and stores mRNAs that will be used only after
fertilization. These messages stay in a dormant state until they are activated
by ionic signals that spread through the egg during ovulation or sperm
binding.
• In many species (including sea urchins and Drosophila), maintenance of the
normal rate and pattern of early cell divisions does not require a nucleus;
rather, it requires continued protein synthesis from stored maternal mRNAs.
• In some instances, these messages are prevented from being translated by
the binding of some inhibitory protein.
• In other instances, the translatability of the mRNA is regulated by the length
of its poly(A) tail. In oocytes, having a short poly(A) tail does not lead to the
degradation of the message; however, such messages are not translated.
• Other organisms use ingenious ways of regulating the translatability of their
messages. The oocyte of the tobacco hornworm moth makes some of its
mRNAs without their methylated 5´ caps. In this state, they cannot be
efficiently translated. However, at fertilization, a methyltransferase completes
the formation of the caps, and these mRNAs can be translated.
Control of RNA expression by cytoplasmic localization
Not only is the time of mRNA translation regulated, but so is the place of RNA
expression.
• The selective localization of messages is also often accomplished through
their 3´ UTRs, and it is also often performed in oocytes.
• There are certain mRNAs in Xenopus embryos that are selectively transported
to the vegetal pole of the frog oocyte. After fertilization, these messages
make proteins that are found only in the vegetal blastomeres.
• In Drosophila, the bicoid and nanos messages are each localized to different
ends of the oocyte. The 3´ UTR of the bicoid mRNA allows this message to
bind to the microtubules through its association with two other proteins
(swallow and staufen). If the bicoid 3´ UTR is attached to some other message,
that mRNA also will be bound to the anterior pole of the oocyte.
• The 3´ UTR of the nanos message similarly allows it to be transported to the
posterior pole of the egg, where it will be bound to the cytoskeleton.
• This localization allows the Bicoid protein to form a gradient wherein the
highest amount of it is at the anterior pole, while the Nanos protein forms a
gradient with its peak at the posterior pole; the ratio of these two proteins
will determine the anterior-posterior axis of the Drosophila embryo and adult.
Post-translational gene regulation
• When a protein is synthesized, its journey is still not over.
• Once a protein is made, it becomes part of a larger level of organization. It
may become part of the structural framework of the cell or be involved in one
of the enzymatic pathways for the synthesis or breakdown of cellular
metabolites.
• In any case, the individual protein is now part of a complex "ecosystem" that
integrates it into a relationship with numerous other proteins. Thus, several
changes that determine whether or not the protein will be active can happen.
• Some newly synthesized proteins are inactive without the cleaving away of
certain inhibitory sections. This is what happens when insulin is made from its
larger protein precursor.
• Some proteins must be "addressed" to their specific intracellular destinations
in order to function. Proteins are often sequestered in certain regions, such as
membranes, lysosomes, nuclei, or mitochondria.
• Some proteins need to assemble with other proteins to form a functional unit
e.g. hemoglobin protein, the microtubule, and the ribosome
• Some proteins are not active unless they bind an ion (e.g. Ca), or are modified
by the covalent addition of a phosphate or acetate group.
Key points in Principles of Development: Genes and development
• Differential gene expression from genetically identical nuclei creates
different cell types. Differential gene expression can occur at the levels of
gene transcription, nuclear RNA processing, mRNA translation, and protein
modification.
• Genes are usually repressed. Activation of a gene often means inhibiting
its repressor. This leads to thinking in double and triple negatives
Activation is often the inhibition of the inhibitor; repression is the
inhibition of the inhibitor of the inhibitor.
• Eukaryotic genes contain promoter sequences to which RNA polymerase
can bind to initiate transcription. The eukaryotic RNA polymerases are
bound by a series of proteins called basal transcription factors.
• Eukaryotic genes expressed in specific cell types contain enhanceR
sequences that regulate their transcription in time and space.
• Specific transcription factors can recognize specific sequences of DNA in
the promoter and enhancer regions. They activate or repress transcription
from the genes to which they have bound.
Key points in Principles of Development: Genes and development
• Enhancers work in a combinatorial fashion. The binding of several
transcription factors can act to promote or inhibit transcription from a
certain promoter. In some cases transcription is activated only if both
factor A and factor B are present, while in other cases, transcription is
activated if either factor A or factor B is present.
• A gene encoding a transcription factor can keep itself activated if the
transcription factor it encodes also activates its own promoter. Thus, a
transcription factor gene can have one set of enhancer sites to initiate its
activation and a second set of enhancer sites (that bind the encoded
transcription factor) to maintain its activation.
• Often, the same transcription factors that are used during the
differentiation of a particular cell type are also used to activate the genes
for that cell type's specific products. For instance, Pax6 is needed both for
the differentiation of the lens and for the transcription of the lens
crystallin genes, and Mitf is needed for pigment cell differentiation and for
the transcription of the genes whose products catalyze the synthesis of
melanin.
• Enhancers can act as silencers to suppress the transcription of a gene in
inappropriate cell types.
Key points in Principles of Development: Genes and development
• Locus control regions may function by making relatively large portions of a
chromosome accessible to transcription factors.
• Transcription factors act in different ways to regulate RNA synthesis. Some
transcription factors stabilize RNA polymerase binding to the DNA, some
disrupt nucleosomes, and some increase the efficiency of transcription.
• Transcription correlates with a lack of methylation on the promoter and
enhancer regions of genes. Methylation differences can account for
examples of genomic imprinting, wherein a gene transmitted through the
sperm is expressed differently from the same gene transmitted through
the egg.
• Dosage compensation enables the X chromosome-derived products of
males (which have one X chromosome per cell in fruit flies and mammals)
to equal the X chromosome-derived products of females (which have two
X chromosomes per cell). This compensation is accomplished at the level
of transcription, either by accelerating transcription from the lone X
chromosome in males (Drosophila) or by inactivating a large portion of
one of the two X chromosomes in females (mammals).
Key points in Principles of Development: Genes and development
• X chromosome inactivation in placental mammals is generally random and
involves the activation of the Xist gene on the chromosome that will be
inactivated.
• Differential RNA selection can allow certain transcripts to enter the
cytoplasm while preventing other transcripts from leaving the nucleus.
• Differential RNA splicing can create a family of related proteins by causing
different regions of the nRNA to be read as exons and introns. What is an
exon in one set of circumstances may be an intron in another.
• Some messages are translated only at certain times. The oocyte, in
particular, uses translational regulation to set aside certain messages that
it transcribes during egg development but uses only after the egg is
fertilized. This activation is often accomplished either by the removal of
inhibitory proteins or by the polyadenylation of the message.
• Many messenger RNAs are localized to particular regions of the oocyte or
other cells. This localization appears to be regulated by the 3´ untranslated
region of the mRNA.