Gene Expression
Chapter Eleven
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
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
A
C
B
E
C
D
A
C
E
D
E
Protein Folding
• Sometimes protein sequence can fold in
more than one way
Sequence
Structure 1
Function A
Structure 2
Function B
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.
2.
3.
4.
5.
6.
7.
8.
Transcription Factors
Methylation
Acelylation
Chromatin and histones
RNAi
Exon shuffling
Alternative Splicing
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
– Platelets
Pathway 3
• Think about disease or sickness
1
2
3
Bone vs. Eyeball?
• Developing organs depends on:
– Differential gene expression
– At specific developmental time points
Bone vs. Eyeball?
All of these levels of
control are happening
Each controlled by:
• Developmental time
points
• Differences in tissue
types
• Differences in genetic
sequence
1. Transcription
Factors
2. Methylation
3. Acelylation
4. Histones
5. RNAi
6. Exon shuffling
7. Alternative Splicing
8. Protein folding
Proteomics
• Study of the structure and function of
proteins, including the way they work and
interact with each other inside cell
• Also - analysis of the protein complement
of the genome
• Or in other words, which proteins are
expressed
• And at what level?
Example from Proteomics
One Gene – Many Proteins
1. Exon Shuffling
2. Protein Folding
3. Genes in both directions
– Another gene lies hidden in the opposite
direction
– When DNA is read 5’ to 3’ (non-coding
strand) will form a second protein
4. Genes within introns
– A second gene is hidden inside the introns
of first
What else is in the Genome?
• Only 1.5 % of genome is actually encoding
genes
• What is the other 98.5 % then?
– Regulation sequences: promoters, enhancers,
repressors, etc
– Noncoding RNA – tRNA, rRNA, etc
– Introns – regulation? other genes?
– Repeats – unknown function
(Some believe repeats are leftovers from
evolution)
What else is in the Genome?
Genes
Regulation
Repeats
Introns
Non-coding RNA
Summary
• Gene expression – is when a gene is
transcribed and translated into a functional
protein
• Regulation of expression happens at:
– DNA, RNA and protein level
• Learn 8 different methods to regulate gene
expression and be able to tell them apart
• Know how one gene can lead to many
proteins
Next Class:
• Read Chapter Twelve
• Homework – Chapter Eleven Problems;
– Review: 1,3,4,7,13,15
– Applied: 3,4,6,8