Gene Expression

Differentiation
• Differentiation is a process where a cell acquires specialized
ability but lose its ability to divide and acquire other specialty
again.

• During differentiation, different types of cells acquire a

distinctive appearance and contain unique materials.

• It should be noted that only embryonic stem cells are the least
differentiated and could become any cell types.
•
• Other cells, even though not yet fully specialized have partly
lose their differentiation ability.

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 What is Gene Expression?
• When a gene is expressed – that gene’s protein
product is made:
1. DNA is transcribed into RNA
2. RNA is translated into Protein
3. Protein is folded and transported so it is functional
• When a gene is not expressed – these steps do not
happen
• Gene is “silenced” – function is off
Gene Expression
 Structural genes or Protein-encoding genes encode
the amino acid sequence of a polypeptide
 Transcription of a structural gene produces messenger
RNA, usually called mRNA
 The mRNA nucleotide sequence determines the amino
acid sequence of a polypeptide during translation
 The synthesis of functional proteins determines an
organisms traits

 This path from gene to trait is called the central

dogma of genetics
The central dogma of genetics
• At the molecular level, a gene is a segment of
DNA used to make a functional product
• either an RNA or a polypeptide

• Transcription is the first step in gene expression

 What is Gene Expression?
• We all have the same genes:
• Different races
• Apes and Humans
• Fruit Flies and Humans
• Different cell types – bone vs. eyeballs
• So what makes us so different?
• It’s not what genes we are carrying
• It’s how and when those genes are expressed
 Questions to ask…
1. How does a bone cell know to express the proteins
that make it a bone, and not an eyeball?
2. How do blood stem cells know when to become
red blood cells, white blood cells or platelets?
3. What makes us human and them apes?

What regulates gene expression?

How is expression regulated?
• Transcription Factors – bind specifically to gene’s
promoters – turn on and off
• Methylation – silencing of huge sections of DNA
• Acelylation – activating huge sections of DNA
• Chromatin and histones – bound will cause a gene
to be silenced
How is expression regulated?
• RNAi – small pieces of RNA bind to mRNA and
effectively remove it before it can be translated into
protein
• Exon shuffling – one gene encodes for different
proteins – depends on which exons translation
machinery “keeps”
• Protein folding – one protein can be folded differently
to have different functions – depends on enzymes
and chaperones
How is expression regulated?
All levels of transcription and translation are involved:
1. DNA sequence will encode for specific regulation –
promoters, exons/introns, etc
2. RNAs – will affect which genes complete the process
to become proteins
3. Proteins – function as enzymes and machinery to
activate or silence specific genes
Transcription Factors
• Proteins that bind:
• Promoters
• Enhancers or Repressors
• Initiate transcription by bringing over RNA
Polymerase and other proteins to the start site of
transcription
• Or repress transcription by blocking proteins from
binding at start site
 Methylation and Acetylation
• Methylation adds -CH3
• Acetylation adds -CO2CH3
• Methylation causes DNA to be silenced:
• Heterochromatin (darker stained regions of chromosomes)
• Example = Imprinting
• Acetylation causes DNA to be activated:
• Move histones away from transcription start site
Histones
• Histones are proteins that wrap up DNA in order to
condense it into Nucleus
• When Histones are binding DNA ?
DNA is silenced:
• RNA Polymerase can’t bind
• When Histones come off DNA ?
DNA is free to be expressed:
• RNA Polymerase can bind – transcription
 RNAi
• Sometimes small interfering RNAs are made
• siRNA
• They will bind to mRNA
• Based on complementary base pairing
• mRNA and siRNA complex will be destroyed
• Therefore mRNA cannot be translated into protein
 Exon Shuffling
• One gene can choose different exons and skip past
others
• Therefore one gene can make many different proteins
• The transcription and translation machinery will
regulate which exons to are used and which are
skipped
• Depending on tissue and developmental time point –
different proteins made
Exon Shuffling
 Alternative Splicing
• Many mRNA sequences can be spliced differently
• Thereby producing more than one protein from same
sequence

Promoter A B C D E

A B C E A C D E
Protein Folding
• Sometimes protein sequence can fold in more than
one way

Sequence
Structure 2
Structure 1
Function B
Function A
 Protein Folding
• One protein sequence can be folded in more than one
way
• Depends on:
• Enzymes
• Chaperone proteins
• Different enzymes will be present in different tissues
or at different developmental time points – therefore
forming different proteins depending
How is expression regulated?
1. Transcription Factors
2. Methylation
3. Acelylation
4. Chromatin and histones
5. RNAi
6. Exon shuffling
7. Alternative Splicing
8. Protein folding
Hemoglobin Subunits
Excellent example of gene expression regulation
• Hemoglobin is a protein
• Made of four subunits
• Each subunit carries
a “heme” group
• Transports Oxygen
• Bound to Iron
Hemoglobin Subunits
During development mammals receive oxygen from
different sources:
1. Embryonic – oxygen comes directly from
mother’s tissues
2. Fetal – oxygen comes through placenta
3. Adult – oxygen comes through lungs
Hemoglobin subunits change according to
developmental time point to handle this
Hemoglobin Subunits
Hemoglobin subunits:
1. Embryonic – 2 epsilon and 2 zeta subunits
2. Fetal – 2 alpha and 2 gamma subunits
3. Adult – 2 alpha and 2 beta subunits
“Locus Control Region” produce proteins that
oversee the assembly of hemoglobin and which
subunits are used
 Blood Cell Types
• In bone marrow – one pluripotent stem cell
• Can make different types of cells
• Has to choose between becoming:
• Red Blood Cell
Filled with hemoglobin
• White Blood Cell
Protecting the body from infection
• Platelets
Blood clotting
Blood Cell Types
• Actually this is more accurate:
 Blood Cell Types
• Bone Marrow – pluripotent stem cell
• Choice based on gene expression:
• Red Blood Cell
Bone marrow activates pathway 1
• White Blood Cell
Pathway 2 1
• Platelets 2
Pathway 3
3
• Think about disease or sickness
Bone vs. Eyeball?
• Developing organs depends on:
• Differential gene expression
• At specific developmental time points
 Bone vs. Eyeball?
All of these levels of 1. Transcription
control are happening Factors
Each controlled by: 2. Methylation
• Developmental time 3. Acelylation
points 4. Histones
• Differences in tissue 5. RNAi
types
6. Exon shuffling
• Differences in genetic
7. Alternative Splicing
sequence
8. Protein folding