1. Gene Regulation
Expression in Eukaryotes & Prokaryotes
SDK
March 30, 2013
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2. Gene Regulation in Prokaryotes
and Eukaryotes
 Gene is the sequence of nucleotides in DNA that
code one mRNA molecule or one polypeptide chain
 In prokaryotes the primary control point is the
process of transcription initiation
 In eukaryotes expression of gene into proteins can
be controlled at various locations.
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3. Check Points for Gene Expression in
Eukaryotes
1. Synthesis of proteins is controlled right from the
chromatin stage.
2. Expression of gene is controlled at many steps
during the process of transcription and translation.
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4. 1.Chromatin Structure
Two forms of chromatin
Euchromatin – A lesser coiled transcriptionally
active region which can be easily accessed by the
RNA polymerases.
Heterochromatin – A highly condensed
transcriptionally inactive region. The genes in this
region cannot be accessed by the RNA
polymerases for active transcription.
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5. 1.Chromatin Structure
Mechanisms which affect the chromatin structure
and hence the expression of gene are:
1.Histone modifications – These modifications
make a region of gene either transcriptionally
active or inactive.
a)Acetylation(addition of an acetyl (CH3CO) group to one of the histone)
• ↑Acetylation ----↓ Condensation of DNA ----- ↑
Transcription of genes in that region
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6. 1.Chromatin Structure
b. Methylation
• Methylation of histone H4 on R4 (arginine residue at
the 4th position) →→ opens the chromatin structure
→→ leading to transcriptional activation
• Methylation of histone H3 on K4 and K79 (lysines
residues at the 4th and 79th position) →→ opens the
chromatin structure →→ leading to transcriptional
activation
• Methylation of histone H3 on K9 and K27 (lysines
residues at the 9th and 27th position) →→ condenses
the chromatin structure →→ leading to transcriptional
inactivation
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7. 1.Chromatin Structure
a) Ubiquitination
Ubiquitination of H2A – Transcriptional inactivation
Ubiquitination of H2B - Transcriptional activation
2) Methylation of DNA
 Target sites of methylation are - The cytidine residues
which exist as a dinucleotide, CG (written as CpG i.e
Cytosine bound to guanine by phosphodiester bond).
 ↑methylated cytidine -- ↓Transcriptional activity
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8. 2.Regulation of Transcription
• The differences in the mechanisms by which the
transcription of gene is controlled in prokaryotes
and eukaryotes are listed below:
Prokaryotes Eukaryotes
The linked genes are organized
into clusters known as operons
which are under the control of a
single promoter.
Eukaryotic genes are not
organized into operons and
each of these genes requires its
own promoter.
These genes are primarily
regulated by repressors.
Regulation by repressors is very
occasional and the primary role
of regulation is played by the
transcriptional activators known
as transcription factors.
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9. 2.Regulation of Transcription
Prokaryotes Eukaryotes
A promoter sequence which
controls an operon lies upstream
of the operon.
Accessory or the regulatory
proteins control the recognition of
the transcriptional initiation sites
by RNA polymerases
Those genes which code
for a protein have a basic
structure consisting of:
Exons – Gene sequences which
encode for a polypeptide
Introns – These sequences will
get removed from the mRNA
before it gets translated.
A transcription initiation site
Promoter sequences.
A single operon gets transcribed
into a polycistronic mRNA which
can be translated into multiple
proteins
Monocistronic mRNAs which can
produce a single polypeptide are
produced
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10. 10
2.Regulation of
Transcription
Promoters
The region necessary to initiate transcription.
Consists of short nucleotide sequence that
serve as the recognition point for binding of
RNA polymerase.
Located immediately adjacent to the genes
they regulate.

11. 2.1: Promoters
Promoters
Prokaryotes - There are two promoter elements or
DNA sequences which are 35 and 10 base pairs in
length and seated upstream to the transcriptional
initiation sites.
The consensus sequence present at
-35 position is TTGACA
-10 position is TATAAT. This is also termed as Pribnow-
box.
Eukaryotes – There are two types of promoters
which are:
Basal promoters
Upstream promoters
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12. 2.2: Promoters
 Basal promoter or core promoter -These promoters
reside within 40bp upstream of the start site. These
promoters are seen in all protein coding genes.
Examples are CCAAT-boxes and TATA-boxes
1. TATA box
 The consensus sequence for TATA box is
TATAT/AAT/A
 It resides 20 to 30 bases upstream of the
transcriptional start site
 This is similar in sequence to the prokaryotic
Pribnow-box
 Proteins like TFIIA, B, C interact with this TATA box
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13. 2.3: Promoters
2. CCAAT-box
 The consensus sequence for this is
GGT/CCAATCT
 It resides 50 to 130 bases upstream of the
transcriptional start site
 Protein named as C/EBP (CCAAT-box/Enhancer
Binding Protein) binds this box
 Upstream promoters - These promoters may lie up to
200bp upstream of the transcriptional initiation site. The
structure of this promoter and the associated binding
factors keeps varying from gene to gene
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14. Promoters
Promoters for RNA polymerase II
include:
TATA box,
CAAT box,
GC box,
& Octamer box.
Site Structure Importance
TATA box -25 30bp upstream
)from the initial
point of
transcription
8bp sequences
composed only of
T=A pairs.
Mutations in this
sequence greatly
reduce transcription
)Loosing the ability
to bind to
transcription
factors(
CAAT box -70 80bp upstream
)from the initial
point of
transcription
CAAT or CCAAT
sequence.
Mutations in this
sequence greatly
reduce transcription
GC box 110bp upstream
)from the initial
point of
transcription
GGGCGG sequence,
often present in
multiple copies.
Documented by
mutational analysis
Octamer box -120 130bp
upstream
)from the initial
point of
transcription
ATTTGCAT
sequence.
Affects the
efficiency of
promoter in
initiating
transcription.

15. 3. Enhancers
DNA sequences interact with regulatory proteins
increase the efficiency of initiation
of transcription
increase its rate.

16. 3.1:Enhancers:
1. Large ) up to several hundred bp long).
2. Tissue- specific ( stimulate transcription
only in certain tissues).

17. 3.2: Enhancers
 Enhancers
Enhancers can be located upstream, downstream or
within the gene that is transcribed
The binding of these enhancers with enhancer
binding proteins (transcription factors) increases the
rate of transcription of that gene to a greater extent.
Promoters are capable of initiating lower levels of
transcription.
Enhancers are responsible for the cell or tissue
specific transcription.
Each enhancer has its own transcription factor that it
binds to.
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18. 3.3: Enhancers
1. The proteins that bind to enhancers affect the activity of
proteins that bind to promoters.
2. Enhancers may allow RNA polymerase to bind to DNA and
move along the chromosome till it reaches a promoter site.
3. May respond to molecules outside the cell ( e.g : steroid
hormones).
4. May respond to molecules inside the cell ( e.g : during
development thus the gene participates in cell
differentiation).

19. 3.4:How enhancers can control transcription
although they are located away from the
transcription site.
Enhancers bind to transcription factors by at
Least 20 different proteins
Form a complex
change the configuration of the chromatin
folding, bending or looping of DNA.

20. 3.5:Action of an enhancer
 – An enhancer binding protein has two binding
sites
Binds DNA
Binds the transcription factors that are bound to the
promoter
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23. DNA looping will bring the distal enhancers
close to the promoter site to form
activated transcription complexes,
then the transcription is activated,
increasing the overall rate of RNA synthesis.
3.6:Enhancers:

25. 4.Transcription factors
“ Are the proteins that are essential for
initiation of the transcription, but they are
not part of RNA polymerase molecule that
carry out the transcription process”.

26. Function:
Each RNA polymerase requires a number of
transcription factors which help in:
1. Binding of the enzyme to DNA template.
2. Initiation and maintenance of
transcription.
3. Control the rate of gene expression.
Transcription factors

27. Structure & Mechanism of action
These proteins contain 2 functional domains, that
perform specific function.
1. DBD: DNA binding domain: binds to DNA sequences
present in regulatory regions (e.g : TATA
binding protein).
2. AD: Transcriptional activating domain: activate
transcription via protein-protein interaction

29. Types of transcription factors:
1. Basal transcription factors:
The initiation of transcription by RNA polymerase
II requires the assistance of several basal
transcription factors.
Each of these proteins binds to a sequence
within the promoter to facilitate the proper
alignment of RNA polymerase on the template
strand of DNA.

30. The basal TFs must interact with the
promoters in the correct sequence to initiate
transcription effectively.
TFIID is the 1st
basal TF that interact with the
promoter ; it contains TATA- Binding Protein.
Followed by TFII B, F, E, H & J.
Types of transcription factors:

32. 2. Special TFs:
Involved in regulation of heat, light, and hormone inducible
genes.
They bind to:
a. enhancers.
b. Basal TFs.
c. RNA polymerase that bind to the gene promoter.
Therefore, special TFs can regulate the transcriptional activity
of the gene.
Types of transcription factors:

33. How is the gene transcription controlled
at this point
• The unique combination of the promoter
sites, transcription factors and enhancers
chosen ultimately decides which gene
gets switched on and which one gets
switched off.
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34. 5.Regulation of RNA
Processing
 RNA processing involves
Addition of 5' cap
Addition of a 3' poly (A) tail
Removal of introns
 The RNAs which get translated to proteins are
transported out from the nucleus to cytoplasm.
 Depending on the final combination of exons after
splicing different kinds of proteins are obtained
which can perform different functions in the cell.
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35. 5.1:Exon Shuffling
• The functions of two proteins synthesized from the same
mRNA are different in different cells as different
combination of exons exist in different cells.
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36. 6.Regulation of RNA Transport
• Only some RNAs function within the
nucleus whereas all other RNAs which are
meant for protein synthesis have to be
transported from the nucleus to the
cytoplasm via nuclear pores.
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37. 6.1:Regulation of RNA Longevity
• mRNAs from different genes have
different life spans.
• The information of the life span of mRNA
is found in the 3' UTR(Un-translated
Reagion).
• The sequence AUUUA within 3' UTR acts
as a signal for early degradation.
• More the number of times the sequence is
repeated  Shorter the lifespan of mRNA
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three prime untranslated region (3' UTR)
6.1:Regulation of RNA Longevity

39. 6.Regulation of Translation
Translational initiation
The expression of a gene product also depends
on the ability of the ribosome to recognize the
correct AUG codon out of the multiple methionine
codons present in the mRNA.
Control of translational process
In many animals large amounts of mRNAs are
produced by the eggs but all of them do not get
translated until the egg is fertilized.
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40. 7.Post Translational Control Points
Post translational modifications
Functional state of protein depends on
modifications like glycosylation, acetylation, fatty
acylation, disulfide bond formations.
Chaperons
Protein transport
Transportation to the site of action also regulate
gene expression.
Protein stability
The lifespan of a protein depends on the specific
amino acid sequence present within them
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41. Summary of the Class
• The expression of genes is controlled at various levels in
eukaryotes.
• At the chromatin stage the level of condensation
determines whether the genes will remain
transcriptionally active or not.
• The unique combination of the promoter sites,
transcription factors and enhancers regulates the
transcriptional rate of a gene.
• After transcription the gene expression is controlled by
RNA processing.
• The expression of gene is also controlled at the level of
translation and after translation.
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