DNA transcription – RNA synthesis

Regulation of gene expression

Biochemistry I
Lecture 13 2008 (J.S.)
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Eukaryotic transcription and translation are separated in space and time

Prokaryotes
Eukaryotes
DNA

transcription nucleus
exons introns

translation

transcription
pre-mRNA
processing

splicing
mRNA
nuclear export
cytosol
translation

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DNA is a template in RNA synthesis
In DNA replication, both DNA strands of ds DNA act as templates to specify the
complementary base sequence on the new chains, by base-pairing.

In transcription of DNA into RNA, only one DNA strand (the negative
strand) acts as template.
The sequence of the transcribed RNA corresponds to that of the coding
(positive) strand, except that thymidine is replaced by uridine in RNAs.

dsDNA coding strand

5´-P- • • • CACCTGCTCAGGCCTTAGC••• -3´-OH positive strand

template
3´-OH- • ••GTGGACGAGTCCGGAATCG••• -5´-P
negative strand
transcribed RNA
5´-P- • • • CACCUGCUCAGGCCUUAGC••• -3´-OH

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RNA synthesis
Ribonucleoside triphosphates are the substrates for the synthesis.
RNA polymerases (DNA-dependent ribonucleotidyltransferases)
recognize the nucleotide sequences in the template strands, initiate the
synthesis of new chains of RNA without a primer, and catalyze the
formation of 3´-5´ phosphodiester bonds in the complementary transcripts.
The nascent RNA chains grow only in the 5´→ 3´ direction,
antiparallel to the direction of the template strand.

In contradistinction to DNA polymerases, RNA polymerases don´t exhibit any nuclease

(proof-reading) activity so that they cannot correct mismatches.
RNA polymerases have binding sites DNA template
– for the free 3´-OH group, 3´- 5´-P
– for bases of the template strand, and
– for nucleoside triphosphates.
They cleave β-phosphate bond of NuTP binding
sites for
and form 3´-5´ phosphodiester bond.
NuTP
5´-
RNA polymerase

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New 3´-5´ phosphodiester bond originates in the reaction between 3´-OH
group of existing chain and α-5´-phosphate of the incoming nucleoside
triphosphate, diphosphate is released (complexed with Mg2+ ions).

Template strand DNA

Direction of RNA synthesis

α (movement of RNA polymerase)
β
γ
RNA-DNA hybrid

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 RNA polymerases
(DNA-dependent nucleotidyltransferases, transcriptases)
In prokaryotes, RNA is synthesized by a single kind of RNA polymerase.
RNA polymerase from Escherichia coli consists of five subunits of four kinds, one
of which is the σ factor that helps find a promoter site where the transcription
begins (and then dissociates from the rest of the enzyme.

In eukaryotes, the nucleus contains three types of RNA polymerase.

The mechanism of their action is the same, but they differ in binding onto different
promoters (template specificity), location in the nucleus, and also in susceptibility to
inhibitor α-amanitin. RNA polymerases contain from 8 to 14 subunits (Mr > 500 000).
In the mitochondrial matrix, there is the fourth type – mitochondrial RNA polymerase.

RNA polymerase Nuclear location Primary transcripts

pol I nucleolus pre-rRNA 45 S

pol II nucleoplasm pre-mRNAs, some snRNAs
pol III nucleoplasm pre-tRNAs, rRNA 5 S, some snRNAs

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 Amanita phalloides (the death cup) produces α-amanitin
that blocks the elongation phase of RNA synthesis

α-Amanitin is a cyclic octapeptide, in which the sulfinyl group

(oxidized sulfanyl group of the cysteinyl residue) is attached to the
indole ring of the tryptophyl residue.
It is an effective inhibitor of eukaryotic RNA polymerases II and III,
namely that of the polymerase II.

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Transcription of DNA
is a three-phasic process consisting of initiation, elongation, and termination.

Transcription starts at promoters on the DNA template.

Promoters are sequences od DNA that direct the RNA polymerase to the proper
initiation site for transcription. Each of the three types of RNA polymerase has distinct
promoters.
Promoters are mostly in the normal upstream position to the initiation site.
The effectiveness of promoters can be regulated (increased or restrained) by
specific DNA sequences called enhancers or silencers that may be distant
up to 2000 base pairs from the promoter either upstream or downstream.
Promoters and enhancers are referred to as cis-acting elements, because they are
sequences of the same molecule of DNA as the gene they regulate.
The DNA sequences of cis-acting elements are binding sites for proteins
called transcription factors.
If those factors are encoded by a gene on a DNA molecule other than that containing
the gene being regulated, they are called trans-acting factors.

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 Eukaryotic promoter site
for RNA polymerase II transcription unit
(the transcribed DNA sequence)
promoter
positive strand start of transcription
5´- GGCAATC ATATAA
3´-
template strand ~ –100 –25 –1 +1
coding region

CAAT box TATA box

(sometimes present) (Hogness box)
in basal gene expression directs TF II D and
specifies the frequency of initiation RNA pol II to the correct site

Polymerase II and transcription factors bound onto the promoter form a complex
called the basal transcription apparatus. It regulates basal gene expression.
Genes that are regulated wholly in this way are constitutively expressed genes
(products of which are most constitutive proteins).
Specifically regulated expression of numerous genes is mediated by various
gene specific transcription factors. Those proteins (coactivators, corepressors,
transcoactivators, etc.) bind to regulatory DNA sequences distant from promoters.
The basal transcription apparatus is thus regulated through direct or mediated contact
with the gene specific transcription factors. See "Regulation of gene expression".
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Transcription initiation
Initiation begins with the binding of TF II D (transcription factor D for pol II)
to the TATA box. TF IID provides docking sites for binding of other transcription
factors. One of those factors is an ATP-dependent helicase that separates the
DNA duplex for the polymerase II, the last but one component of the basal
transcription apparatus. Pol II contains an unphosphorylated carboxy-terminal
domain (CTD).

CTD
pol II
TF II D

transcription unit

promoter unwound DNA (~17 bp opened)

Polymerase II with its unphosphorylated CTD then slides to the start of

transcription and initiate transcription by producing short transcripts consisting of
not more than 20 – 25 nucleotides.

After the transcription is initiated, most transcription factors are released from pol II.
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Switch from initiation to elongation
is driven by phosphorylation of carboxy-terminal domain of pol II

+1

CTD is then phosphorylated. The resulting change in conformation of pol II (from

pol II A to pol II O form) enables binding of capping enzyme (CE) to pol II and
methyltransferase (MT) to CE. Both those enzymes modify the 5´-end of the nascent
transcript to 5´-m7Gppp-cap required for the further progress in transcription.
The phosphorylated CTD of pol II has a central role in cotranscriptional
RNA processing, because it also binds, in addition, splicing factors and factors
responsible for the final polyadenylation of the transcripts.

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Elongation phase

dsDNA rewinding unwinding

3´
template strand
5´

RNA-DNA hybrid elongation site

nascent transcript

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Termination
In prokaryotes, termination signals usually contain
a palindromic GC-rich region and an AT-rich region.
Thus the mRNA transcripts of this DNA palindrome
can pair to form a hairpin structure with a stem and
loop followed by a sequence of more uracil base –
RNA transcripts end within or just after them

In eukaryotes,
no perspicuous termination signal has been found.
Transcripts produced by DNA polymerase II are released from the transcription
apparatus after the polyadenylation signal AAUAAA and the GU- or U-rich
sequence that is able to bind cleavage stimulation factor (CStF) had been
transcribed. The terminal sequences of the transcripts are decomposed in the
course of 3´-polyadenylation (not encoded by template DNA).

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Polyadenylation of transcripts
Cleavage-and-polyadenylation
specifity factor (CPSF) binds onto an
polyadenylation signal AAUAAA.

It is not quite clear when transcripts are

released from the transcription apparatus.

A downstream GU- or U-rich sequence binds

the cleavage stimulation factor (CStF) and
cleavage factors (CF 1,2), a loop is formed.

cleavage
Binding of poly(A) polymerase (PAP) then
stimulates cleavage at a site about 20
nucleotides downstream the polyadenylation
signal. The cleavage factors are released, the
cleaved RNA chain degraded.

Poly(A) polymerase adds 12 adenylate

residues, elongation is provided by transfer of
many short poly(A) chains from poly(A)-binding
protein.
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The transcription products of all three eukaryotic polymerases
are processed before their export from the nucleus
Precursors of rRNA are cleaved in functional rRNA types.
Ribosomal RNA folding pattern (rRNA 18 S)
RNA polymerase I transcribes
45 S pre-RNA within the nucleolus:
45 S pre-rRNA

32-35 S rRNA 20-23 S rRNA

28 S rRNA
18 S rRNA

5.8 S rRNA

The fourth ribosomal RNA 5 S rRNA

is transcribed by RNA polymerase III
within the nucleoplasm. 15
Examples of tRNA processing:
Modification of somebases ribosyl thymine

methylation

uridine pseudouridine (ϕ)

transformation of
the linkage to ribosyl 5

3´-terminal UU replaced by amino

a leader sequence
acid attachment site CCA-3´-OH
processing

transcript
anticodon
of intron

precursor tRNA mature tRNA

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Cotranscriptional and posttranscriptional processing
of transcripts (pre-mRNA) produced by RNA polymerase II

Primary transcripts of genes transcribed by RNA pol II (precursor mRNAs)

undergo processing, mostly before their transcription is finished:
The 7-methylguanosine "cap“ is attached to the 5´-end triphosphate.
The transcripts of non-coding sequences of the gene (introns) are cut off and the
transcripts of coding sequences (exons) spliced, the process is called splicing.
Termination of transcription is connected with the adding of a polyadenylate chain
to the 3´-end (after cleavage of the terminal sequence of the primary transcript). .

In some mRNAs, the base sequence is altered after transcription by processes other
than RNA splicing. Those processes are called RNA editing and are not very rare
E.g. cytidine residue may be deaminated to uridine, adenosine to inosine.

Processed mRNAs bind certain kinds of proteins and form so complexes called
messenger ribonucleoproteins (mRNP) that are exported through nuclear pore
complexes into cytoplasm.
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 The 7-methylguanosine 5´-cap
prevents mRNA against
5´-endonucleases and it is
also the marker recognized in
proteosynthesis.

Splicing schematically:

pre-mRNA

mRNA

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Splicing
Nucleotide sequences determine the splice sites:

cleavage

U1 U2 U5

5´-2´-phosphodiester bond
between 5´-end of the intron
and branch site Ado forms a lariat

spliceosome
cleavage

joining

Excised intron sequence

is degraded in the nucleus
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There are many types of small RNA molecules with fewer than 300 nucleotides
in the nucleus - small nuclear RNAs (snRNAs). A few of them are essential
for splicing pre-mRNA. They associate with specific nuclear proteins to form
complexes called small nuclear ribonucleoprotein particles (snRNP, "snurps").

During the splicing of pre-mRNA, the processed mRNA, snRNPs U1, 2, 4, 5, 6,

and other protein splicing factors form large assemblies (about 60 S) termed
spliceosomes.

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Export of messenger ribonucleoprotein particles (mRNPs)
through the nuclear pore complex

For the transport, messenger ribonucleoprotein particle (mRNP) associates with

the heterodimer known as the general mRNA export receptor (exportin 1).
The nuclear pore complex consists of proteins nucleoporins, which contain Phe-
Gly repeats and zinc-finger domains. These structures provide transient docking
sites for the complex export receptor - mRNP traversing the nuclear pore "basket".
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Regulation of gene expression

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Gene expression is the term that involves conversion of the genetic
information encoded by a gene into the final gene product,
i.e. a protein or a functional RNA (rRNA, tRNA).
Control of gene expression in prokaryotes differs from that in
eukaryotes distinctly.

Gene expression in prokaryotes

In prokaryotes, gene activity is controlled foremost at the level of transcription, at
its initiation.
The structural genes are usually grouped together in operons, which are
transcribed from one promoter controlled by a regulatory protein.

Regulator gene Operon

operator
==== ===
prom. promoter structural genes

mRNA polycistronic mRNA

regulatory protein protein 1 protein 2 protein 3 protein4

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Negative control of transcription in prokaryotes
is based on the existence of regulatory proteins named repressors (products of
specific regulatory genes) that bind onto specific operator sequences within the
promoters and prevent from binding RNA polymerase and initiation of
transcription of genes of the regulated operon.
Repression of gene expression
In repressible transcriptions, repressor proteins are produced usually in their
inactive forms. They are able to bind onto specific operons and act as
active repressors only in the presence of co-repressors, allosteric activators,
which change their conformation.
Repressible operons are oft those, which provide enzymes for biosynthetic
pathways that can be blocked by the presence of product of the synthesis.
Induction of gene expression
In inducible transcription, the regulatory protein repressor in produced
constitutively and is bound to the operator, transcription of the gene cannot
occur: inducers are allosteric effectors, which bind the repressors and
lower their affinity for the operator. In the presence of the inducer, the
repressor leaves the operator and transcription of the gene begins. So induction
in prokaryotes is derepression in fact.
Inducible operons are mostly those providing enzymes of catabolic pathways
(operon expressed only in response to the presence of substrate).
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Examples of negative control in prokaryotes:

Induction of E. coli lac operon by lactose

The enzymes of glucose metabolism are constitutive (synthesized all the time).
If lactose appears in the medium lacking in glucose, cells begin to produce enzymes
which are able to metabolize lactose (β-galactosidase, permease, and transacetylase).
Inductor is allolactose (formed by spontaneous isomerization of lactose) that binds
to the lac operon repressor and inactivates it.

Repression of E. coli trp operon by tryptophan

The genes encoding five enzymes essential for the biosynthesis of tryptophan are
included in trp operon. Repressor of trp operon is expressed constitutively, but in its
inactive form that in activated by binding tryptophan. Thus the biosynthesis of
tryptophan is inhibited, if there is sufficient tryptophan concentration within the cell.
Tryptophan acts as corepressor of trp operon that prevents from its transcription.

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Positive control of transcription in prokaryotes
Regulatory proteins can act sometimes as activators, which bind near the promoter
and support binding of RNA polymerase to the promoter.
An example of positive control:
In E. coli , transcription of lac operon induced by lactose increases approximately
50 times in the rate in the presence of "catabolite gene activator" protein (CAP)
complexed with cAMP; however, concentration of cAMP in E. coli is high in the
absence of glucose. The consequence is that lactose can be effectively
metabolized only if there is insufficient supply of glucose – the preferred nutrient.
Glucose lowers the concentration of cAMP. cAMP then cannot bind the CAP and
transcription of operon providing enzymes of lactose catabolism is insufficient even in
the presence of the inducer lactose.
This type of positive control of lac operon is known as catabolite repression,
because it disables in the presence of glucose.

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 Regulation of gene expression in eukaryotes
Let us remember the differences between gene expression in prokaryotes
and eukaryotes. In eukaryotes:
– Nuclear DNAs are highly condensed in chromosomes and, in addition,
they interact tightly with histones forming nucleosomes.
– Each gene has its own promoter, there are no operons.
– In primary transcripts, the transcripts of introns are included that have to
be excised.
– Transcription and translation are separated both in space and in time.

The control of eukaryotic gene expression occurs principally at the level

of transcription. However, there are numerous other ways of control:
Regulation at the level of
1 chromatin and DNA,
2 transcription,
3 processing of primary transcripts,
4 translation and posttranslational processing.

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 1 Regulation at the level of chromatin and DNA
Control of the gene accessibility for transcription
Chromatin of chromosomes occurs in two kinds, either as condensed heterochromatin
(the included genes are not active transcriptionally) or diffused euchromatin, the
genes
of which are transcribed. Each cell of the organism (with a few exceptions) contains
the same complement of genes. However, the changes in chromatin structure type
occurring in development and differentiation of tissues and cell types result in
differential gene expression.

Chromatin remodelation
are those changes in organisation of dsDNA in chromatin fibres that are required for
initiation of transcription. Various mechanisms of remodelation exist.
E.g., unwinding of dsDNA segments from nucleosomes depends on both hydrolysis
of ATP and covalent modification of histones (acetylation of ε-amino groups of
lysyl residues at N-ends of histones H2A. H2B, H3, and H4).on se

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Methylation of DNA
Methylation of cytosine base of DNA to 5-methylcytosine occurs oft in the GC-rich
sequences near gene promoters. This modification of DNA is catalyzed by specific
methylases, genes containing 5-methylcytosines are transcribes less easily
than those non-methylated.
Example: The genes for α- and β-globin chains are methylated in non-erythroid
cells that cannot synthesize haemoglobin. In erythroblasts and reticulocytes
(precursors of red blood cells), those genes are not methylated.

Selective gene rearrangements

The coding segments of DNA can recombine within the particular gene or may
associate with other genes within the genome.
Example: Recombination of gene segments type V, J, and C of genes for
immunoglobulins is the cause of vast diversity of specific antibodies.

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Amplification of genes
Eukaryotic genes can be amplified during development or in response to drugs.
Certain parts of chromosomes is repeatedly replicated during particular cell cycle.
Newly synthesized DNA is excised in the form of small, unstable chromosomes (called
double minutes) that are incorporated into other chromosomes.
Amplification occurs normally due to mistakes in DNA replication or cell division.
However, under appropriate conditions, these extra rounds of replication can become
"frozen" in the genome.
Example: In patients receiving methotrexate (inhibitor of dihydrofolate reductase) can
develop drug resistance by increasing the number of genes for dihydrofolate
reductase by gene amplification.

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 2 Regulation at the level of transcription
The most important and fundamental element in the initiation of transcription
is the promoter, on which the basal transcription machinery complex
(basal transcription factors and RNA polymerase) is assembled.
Basal control of transcription
seems to be common to all genes. It includes binding of basal transcription
factors to the promoter or closely adjacent sites. Some of those factors
determine by binding to GC and CAAT boxes how frequently transcription is
to occur.
Specific control of gene expression
Gene-specific or tissue-specific expression depends on
– regulatory DNA sequences within the same DNA molecule
(cis- elements), which can influence transcription even when separated
by thousands of base pair from promoter - enhancers, silencers,
hormone response elements, and
– specific transcription factors – proteins originating from genes
presumably located on different chromosomes (trans-acting elements),
which don´t bind to the promoter or closely adjacent 31
DNA sites.
Regulatory DNA sequences
can either increase (enhancers) or decrease (silencers) the rate of transcription
of eukaryotic genes. This effect is mediated by specific transcription factors.
Enhancers bind transactivators or coactivators, silencers bind corepressors.
Hormone response elements (HRE) are regulatory DNA sequences that bind
complexes of hydrophobic hormones (steroid and thyroid hormones, retinoates)
with there intracellular receptors. They act as enhancers or silencers.
Specific transcription factors
are proteins, which bind to regulatory DNA sequences remote from the promoter.
and act as activators (transactivators or coactivators) or repressors
(corepressors) of transcription of specific gene.
They mediate the effects of enhancers, silencers, and hormone response elements
through interactions with other mediator proteins that interact directly with basal
transcription factors and support or disable transcription of particular genes.
Regulation of the function of transcription factors (both basal and specific)
– The synthesis of transcription factors (down- and up-regulation).
– The effects of transcription factors can be modulated by binding of stimulatory or
inhibitory ligands, and also by cooperation of transcription factors.
– Factors can be phosphorylatred od dephosphorylated owing to various
extracellular signals (growth factors, peptidic hormones, cytokines,
32 etc.).
 Regulation of a typical eukaryotic gene by an enhancer

basal transcription apparatus

specific transcription factors (Pol II and basal factors)

coactivator CTD
TF IID Pol II

~ 2 000 bp
regulatory sequence upstream
promoter

enhancer

coactivator
transactivator

~ 2 000 bp mediator proteins

CTD
TF IID Pol II

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Regulation of transcription by steroid and thyroid hormones

Steroid and thyroid hormones (iodothyronines) are hydrophobic so that they

can diffuse through the plasma membrane into the cells.
Hormones are bound onto specific intracellular receptors.
Complexes of these receptors with hormones are specific transcription
factors. They bind onto regulatory DNA sequences called
hormone response elements (HRE).
The interaction with coactivators and mediator proteins follows and
interaction between mediator proteins and the basal transcription apparatus
initiates (or inhibits) the transcription of particular gene.

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Example: Initiation of transcription by cortisol
Active complex cortisol-receptor binds onto DNA at the specific sequence
GRE (glucocorticoid response element, one of the HRE – hormone response
elements).
The coactivator and specific hormone response element-binding proteins
(HREB-proteins) are also attached. This complex acquires the ability to act as
enhancer that supports initiation of transcription on the promoter by means of
mediator proteins.

cortisol-GR dimer complex

GRE enhancer
GREB protein coactivator

mediator proteins
> 1 000 bp
CTD
Pol II basal
TF IID
transcription
apparatus

promoter

GR dimer – intracellular glucocorticoid receptor (dimer)

GRE – glucocorticoid response element
GREB protein – GRE binding protein (a specific transcription factor)
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Transcription factors that bind onto regulatory DNA sequences
comprise mostly one of the typical structural motifs:
helix-turn (or loop)-helix, zinc-finger, and leucine zipper.
Only the small part of protein molecule (called DNA-binding domain) is responsible
for the interaction with DNA. It is usually represented by two adjacent α-helical
segments.

NRS

helix-turn-helix zinc finger leucine zipper

Zinc finger, e.g., occurs in DNA binding domains of steroid-hormone receptors.

NRS (nucleotide recognition signal) is a part of α-helix containing amino acid
sequence that is able to recognize specific regulatory sequence of nucleotides in
the major groove DNA.

Transcription factors are attached to DNA usually in the major groove.

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 3 Regulation at the level of
processing of primary transcripts
Alternative splicing
Alternative splicing can cause that the products of a sole gene are
various proteins:

RNA editing
In some mRNAs, the base sequence is altered after transcription by processes other
than RNA splicing. Those processes are called RNA editing and are not very rare
E.g., cytidine residue may be deaminated to uridine, adenosine to inosine.

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4 Regulation at the level of translation
is mediated mostly through changes in activities of eukaryotic
initiation factors (eIFs).

Example:
The synthesis of globin in reticulocytes is controlled by phosphorylation
of the initiation factor eIF2. It is active when phosphorylated, inactive
in the dephosphorylated form.
Haem prevents from eIF2 from phosphorylation.
If haem is present within the cell, eIF2 is not phosphorylated - active,
the translation of mRNA for globin chains proceeds.
If there is no haem in the cell, eIF2 is inactive and globin chains are not
synthesized.

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