Control of

gene expression
561 104 Basic Cell and Molecular Biology
Supusson Pengnam, Ph.D.
pengnam_s@su.ac.th
208291

1
 Level of gene expression
Chromosome remodeling (Transcription in Euk)
Epigenetics: behaviors and environment can
cause changes that affect the way your genes
work
Transcription: initiation (Pro/Euk)
Promotor + RNAP + σ/TF
Post transcription:
RNA processing (Euk)
stability & RNAi (Pro/Euk)
transport (Euk)
Translation (antibiotics)
Translation initiation (Pro/Euk)
Translation repressor protein (Euk)
Post translation (Euk)

. 2
https://cnx.org/contents/Q9ip7GS4@17/Regulation-of-Gene-Expression
 Type of gene expression
How does a cell know which genes to express?
Constitutive genes / Housekeeping genes
Genes are switched on all the time because they are needed for maintenance of
essential life function

Express depend on the NEED for gene product, involves in cell development and division.
Repressible genes
Gene involves in the anabolic pathway.
[product]↑ expression ↓ (turn off gene)
Inducible genes
Gene involves in the catabolic pathway.
[substrate] ↑ expression↑ (turn on gene)

3
 Type of transcription regulation

1. Positive regulation
“activator” Positive Negative
regulation regulation
E.g. transcription factor (TF) that increases
activator repressor
the transcription by facilitating RNAP

2. Negative regulation
DNA
“repressor”
E.g. transcription factor (TF) that suppresses
the transcription of a gene

4
 Type of transcription regulation
a small molecule
either activates or represses transcription by interacting with a repressor or an activator.

inactive
+ repressor
+
activator repressor
active
activator

DNA

active
activator

√ √
5
✓ Transcription
ON

X Transcription
OFF

6
Gene regulation in
Prokaryotes

7
 Transcription regulation in prokaryote
“Operon”

Enhancer

Operon = Promotor + Operator + Genes

Regulatory region
Promoter = binding site of RNAP
Operator = binding site of repressor
Enhancer = binding site of activator

Regulator gene produced “repressor”

https://cnx.org/contents/kxd8RhSc@1.9:0keuXsZD@1/Gene-Regulation-Operon-Theory
8
 Type of Operon

Type of Example Metabolic process Effect on Metabolite Repressor Transcription

operon operon

Inducible Lac Catabolic pathway ON Substrate ↑ Inactive ↑

operon operon (breaks down large
molecules) Lactose

Repressible Trp Anabolic pathway OFF Product ↑ Active ↓

operon operon (builds molecules)
Tryptophan

9
 lac operon
(inducible operon)
Regulates catabolism of lactose (break down)
lactose = glucose + galactose
Require 3 structural genes for catabolism of lactose
lacZ: galactosidase
lacY: galactoside permease
lacA: galactoside transacetylase
𝛽-galactosidase galactose enzymes for lactose breaking down
Regulator gene
Lactose glucose lac I
wasteful to create the enzymes if lactose was not available

Regulation of lac operon

1. Inducible Operon (lac I)
+ repressor
inactive ✓ Transcription
repressor
ON

2. Catabolite Activator Protein (CAP)

= cAMP receptor protein
+ CAP ↑↑ Transcription

https://www.youtube.com/watch?v=o3eI8lAQyqM 10
 Lac operon regulation by
1. Inducible Operon (lac I)
No lactose
X Transcription
lac I produce repressor protein RNAP active OFF
repressor

Present of
lactose + repressor

inactive
repressor
✓ Transcription
ON
RNAP
Promoter lac I Promoter Operator lacZ lacY lacA

11
 Lac operon regulation by
2. Catabolite Activator Protein (CAP)

Bending of DNA strand (more

+ space for RNAP to bind easily
CAP (Activator) ↑ RNAP-promotor binding
Low glucose
↑↑ Transcription
CAP
(Activator) RNAP
Promoter CAP CAP site Promoter Operator lacZ lacY lacA

https://cnx.org/contents/kxd8RhSc@1.9:0keuXsZD@1/Gene-Regulation-Operon-Theory#OSC_Microbio_11_07_CAP 12
 Lac operon regulation
cAMP ↑
High
Transcription
cAMP ↑
- glucose
+ lactose
Low
Transcription
+ glucose cAMP ↓
+ lactose
NO
+ glucose cAMP ↓ Transcription

- lactose
cAMP ↑

cAMP ↑
- glucose NO
Transcription

- lactose
13
 Type of Operon

Type of Example Metabolic process Effect on Metabolite Repressor Transcription

operon operon

Inducible Lac Catabolic pathway ON Substrate ↑ Inactive ↑

operon operon (breaks down large
molecules) Lactose

Repressible Trp Anabolic pathway OFF Product ↑ Active ↓

operon operon (builds molecules)
Tryptophan

14
 Trp operon
(Repressible operon)
Regulates anabolism of tryptophan (built)
Require 5 structural genes for anabolism of tryptophan
TrpE, TrpD,TrpC, TrpB, TrpA
enzymes for tryptophan synthesis
Regulator gene
trpR
Regulation of Trp operon
1. Repressible Operon (trpR) active X Transcription
+ repressor
repressor
OFF

2. Attenuation on trpL (leader) X Transcription

OFF

15
 Trp operon regulation by
1. Repressible Operon (trpR)
inactive
repressor

✓ Transcription
ON

X Transcription
OFF
active
repressor

16
 Trp operon regulation by
2. trpL leader region (Attenuator)
Trp operon

Attenuator

DNA TrpL
Leader region

1 2 3 4
Leader
AUG UGGUGG UGA UUUUU
mRNA
Two
Trp codons
● transcriptional-attenuation
Leader peptide
“2 Tryptophan” ● formation of mRNA stem-loops prevents the continuance of
transcription
● based on the levels of tryptophan in the metabolic environment
Leader
mRNA *Position of ribosome along the leader mRNA is crucial*
17
 ✓ Transcription ON

Leader
mRNA
1

Low level of tryptophan → Trp-tRNA ↓, aminoacylation ↓

● Ribosome arrest at 1° Trp codon (region 1)
● region 2&3 complementary = antitermination
● RNAP continues transcription into trp structural gene
● No attenuator structure
https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/7%3A_Microbial_Genetics/7.19%3A_RNA-Based_Regulation/7.19B%3A_Attenuation 18
 X Transcription OFF

Leader

High level of tryptophan → Trp-tRNA ↑

● leader peptide = Trp leader = “2 Tryptophan”
● region 3&4 form stem loop with UUUU
● “Attenuator” = termination signal
● similar to intrinsic terminator of transcription
https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/7%3A_Microbial_Genetics/7.19%3A_RNA-Based_Regulation/7.19B%3A_Attenuation 19
Low level of tryptophan
● Need Trp synthesis
● Ribosome pausing
● Leader forms antiterminator
● Transcription of Trp-genes
High level of tryptophan
● Not need Trp synthesis
● Fast translation of leader mRNA
● Leader forms terminator
● Termination of transcription
20
Low Tryptophan
“ON” trp operon
• No active repressor
• no attenuator loop

mRNA
1

High Tryptophan
“OFF” trp operon • active repressor
• block transcription

Attenuator • Trp leader transcribe

• from attenuator
• Termination of transcription
mRNA
1 2

21
Gene regulation in
Eukaryotes

22
Gene regulation in Eukaryotes

23
 Nuclear receptor
• Lipid-soluble hormone act as transcription factor
e.g. thyroid hormone
sex hormone receptors
steroid receptors
• Diffuse through the plasma membrane
• Bind to nuclear receptor, interact directly with DNA
• Stimulates synthesis of mRNA and codes for specific
protein
• The cell response to Lipid-soluble hormone e.g.
- secretion of new protein
- control gene expression in embryonic
development or adult homeostasis

https://quizlet.com/331498007/endocrine-system-nuclear-receptor-model-diagram/
24
 Epigenetics
Epigenetic effects (not mutation)
● alterations to gene expression
● not caused by changes in the DNA base sequence
● transmission of traits to future generation
(unrelated to changes in nucleotide sequence)
● frequently associated with changes in chromatin structure e.g., chemical modifications
○ DNA acetylation of histone modification
○ DNA methylation

https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/ 25
 Epigenetics
DNA acetylation ↑↑ Transcription
Chromatin remodelling can control gene expression

Enhance → decrease
transcription chromatin condensation

Suppress → increase
transcription chromatin condensation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660019/
26
 Epigenetics
DNA methylation ↓↓ Transcription

Non-methylated → genes active genes

Methylated genes → inactive genes

● Inhibit binding of TF with DNA

● Inhibit RNA polymerase and decrease translation
● Increase chromatin condensation

https://training.galaxyproject.org/archive/2022-05-01/topics/epigenetics/slides/slides-plain.html
27
 Regulation of transcription in Eukaryotes

Activation
Activator prot. + Enhancer seq

Reduction
Repressor prot. + Silencer seq

http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Lekt03bkg.html

Enhancer and Silencer sequence locate near/far from promoter and gene. 28
 2. Post transcriptional control
● RNA processing control
5’ Capping
3’ polyadenylation
alternative splicing
RNA editing
● RNA transport and localization
● mRNA stability / degradation
miRNA
siRNA
29
 Type of RNA

tRNA (transfer RNA)

mRNA (messenger RNA)
rRNA (ribosomal RNA)
housekeeping
RNA ncRNA
snRNA (small nuclear RNA)

ncRNA (non-coding RNA) snoRNA (small nucleolar RNA)

lncRNA
regulatory (long non-coding RNA ≥200 NTs)
ncRNA
small ncRNA (<200 NTs) miRNA (microRNA 19-22 NTs)

Long Noncoding RNAs in Metabolic Syndrome Related Disorders (hindawi.com)

30
 miRNA
(MicroRNA)

● RNA interference
● endogenous single strand
transcript hairpins RNA in
the Nucleus
Cleaved dsRNA by Dicer
Antisense strand

sense strand
●

● mRNA cleavage &

Transcriptional blockage

https://link.springer.com/chapter/10.1007/10_2019_109

31
 RNA interference
miRNA siRNA (Short interfering)
Origin: Origin:
ssRNA comes from endogenous non-coding RNA. exogenous dsRNA uptaken by cells
present in all animals and plants. present in lower animals and plants
but not found in mammals

Structure: 19-25 nucleotide hairpin RNA Structure: 21-23 nucleotide dsRNA

Target: inhibit translation of multiple mRNA targets Target: highly specific with only one mRNA target
because of its imperfection in pairing.

Purpose: miRNA functions as an endogenous gene Purpose: The siRNA is primarily to provide viral
expression regulator defense and genome stability

32
 Translation control
Translation initiation step
● Protein bind to 5′ UTR mRNA and inhibit binding of ribosomes

Translation repressor protein

● Repressor proteins bind to operators and prevent the transcription of structural genes

Post translation
● Cleavage and trimming of amino acids from the ends, by acetylation, the addition of
phosphate groups, carboxyl groups, methyl groups, or carbohydrates to the protein.
● These modifications affect the transport, function, and activity of the proteins and
have the capacity to affect gene expression.

33
 Level of gene expression
Chromosome remodeling (Transcription in Euk)
Epigenetics
behaviors and environment can cause
changes that affect the way your genes work
Transcription: initiation (Pro/Euk)
Promotor + RNAP + σ/TF
Post transcription:
RNA processing (Euk)
stability & RNAi (Pro/Euk)
transport (Euk)
Translation (antibiotics)
Translation factor: initiation (Pro/Euk)
Post translation (Euk)
Modification, stability, transport
.
34
https://cnx.org/contents/Q9ip7GS4@17/Regulation-of-Gene-Expression
35
 Application of these basic knowledge
● Drug discovery, elucidation mechanisms of action of drug
(eg. Antibacterial)
● Production of therapeutic agents and valuable proteins
by recombinant DNA technology
● Understand pathogenesis of various genetic disorders
● Diagnosis, Therapy : stem cell therapy
● Fundamental knowledge for various sciences

36
 References
1. Benjamin A. Pierce. 2012. Genetics: A Conceptual Approach (Forth Edition). W. H. Freeman.
2. David P. Clark, Nanette J. Pazdernik, Michelle R. McGehee. 2019. Molecular Biology (Third Edition).
Academic Cell.
3. Thomas D. Pollard, William C. Earnshaw, Jennifer Lippincott-Schwartz, Graham T. Johnson. 2017. Cell
Biology (Third Edition). Elsevier.

37