Control of Gene Expression 1: Transcriptional Controls Flashcards
What makes a cell different?
There are the same amount of genes (~25,000) but they express different sets of proteins
Each cell has the same genome - differentiation in cells depends on changes in gene expression
What is an experiment that proves there is no loss of genes in cell differentiation?
Take a skin cell from a frog and remove its nucleus.
Take an unfertilized egg and destroy its nucleus by UV light
Inject the nucleus from the skin cell into the empty egg and a normal embryo will form. A tadpole will be produced
What is RNA Seq?
Technology that uses the capabilities of next-generation sequencing to reveal a snapshot of RNA presence and quantity from a genome at a given moment in time
Can look at the different populations of RNA
What gene using RNA seq, showed that many cells including embryonic stem, liver, muscle etc expressed it?
Beta-actin gene
The higher the read the more it is expressed. How many times it sequences the RNA shows that relative expressiveness
Proteins that are common among different cell types are called what?
Housekeeping proteins
e.g glucose metabolism - required by many cells
Proteins that are only found in a few select cell types are called what?
Specifically limited proteins
e.g hemoglobin
A typical human cell expresses how much of its 25,000 genes?
30-60%
But level of gene expression varies
Different cell types expressing different genes and level of gene expression can be used in what procedures?
Fingerprint expression profiles
microarrays
or RNA Seq
What are factors that can change gene expression post transcription?
Alternative splicing (dystrophin gene), post translational modification
What does gene regulation require?
Short stretches of DNA of defined sequence (recognition sites for DNA binding proteins)
and gene recognition sequences for regulatory proteins
What is the master control protein for the production of red blood cells? What is its recognition sequence?
GATA1
TGATAG
Where can recognition sequences be relative to first exon?
Proximal or distal (e.g 50 kb away)
In DNA motif recognition regulatory proteins associate with what?
major groove
What do proteins recognize and bind to in major groove?
bases: major groove presents a specific face for each of the specific base pairs
CTGA
A gene regulatory protein recognizes a specific ______
DNA sequence
The surface of the regulatory protein is extensively _________ to the surface of the DNA region to which it binds
complementary
A series of contacts is made with the DNA involving ___ possible configurations
4
In the possible configurations of base pairs what does Blue stand for?
Possible hydrogen bond donors
In the possible configurations of base pairs what does Red stand for?
Possible hydrogen bond acceptors
In the possible configurations of base pairs what does the yellow stand for?
methyl groups
In the possible configurations of base pairs what does the white stand for?
Hydrogen atom
Gene regulatory proteins read the ____ of the DNA helix
outside
What does a typical gene regulatory protein-DNA interaction involve?
10-20 interactions
Sequence specific transcription factors are considered to be what?
modular: domains that have specific jobs to do
What are the four possible modules of a DNA transcription factor?
DNA-Binding module
Dimerization module
Activation Module
Regulatory Module
(Every/not every) transcription factor will have all modules
Not every
A transcription factor will have what 2 modules?
DNA-binding module
and activation module
What two modules COULD (optional) transcription factors possibly have?
Dimerization and regulatory modules
What experiment provided evidence for transcription factors being modular?
ESSAY
Yeast study
Two plasmids: reporter gene construct (DNA target) It is going to report of a promotor and gene is active (gene is the lacZ gene)
and experimental plasmid (making transcription factor) that binds to
UAS=upstream activation sequence
Take a full protein- this protein has this one has two modules. How do we find that out? Create plasmids that have deletions and see if previous actions are not taking place.
Example of a result: If DNA-binding domain is deleted then Binding to UAS will not happen. as a result then there will be no GAL4 protein activity
What are the four most common DNA-binding domain structural motifs?
Helix-turn-helix
Zinc finger motif
Leucine zipper
Helix-loop-helix
*also homeodomain and beta-sheet
What is the simplest most common DNA-binding motif?
Helix-turn-helix
Describe Helix-turn-helix
- two alpha helices connected by a short chain of amino acids that make the “turn” -turned at fixed angle
Which helix of helix-turn-helix is the DNA binding module?
The longer helix, it fits into major groove
The side chains of amino acids recognize DNA motif
Most of the time Helix-turn-helix motifs bind as what?
Symmetric dimers: bind DNA as dimers
Describe the Zinc finger domain
Binds to major groove of DNA
DNA binding motif includes Zn atom
If you draw out amino acid sequences, the cartoon looks like a finger projection-hence the name
3D structure looks NOTHING like a finger projection
What can Zn finger domains be found in?
Tandem clusters - This allows multiple contact points and thus, This stabilizes the contact/interaction it has with DNA
What domains does a leucine zipper motif have?
Dimerization domain
Activation Domain
and DNA binding domain
Describe Leucine zipper motif structure and how it binds to DNA
Two alpha helical DNA binding domains
Dimerizes through leucine zipper region (homo-/hetero-)
Activation domain overlaps dimer domain
Grabs DNA like a clothespin
What forms the zipper in leucine zipper motif?
Interactions between hydrophobic amino acid side chains (leucines)
Leucine residue every 7 amino acids down one side of alpha helix dimerization domain: forms zipper
What does a helix-loop-helix domain consist of?
A short alpha chain connected by a loop to a second longer alpha chain
Describe Helix-loop-helix domain
Can occur as homodimers or hetero
Three domains or moddules to this protein: DNA binding, dimerization, and activation domain
What is hereditary spherocytosis?
A hemolytic anemia characterized by spherical and fragile red blood cells that lyse and release hemoglobin
What are the clinical presentations of someone with hereditary spherocytosis?
Hemolysis, anemia, and splenomegaly(enlarged spleen-red blood cell producing factory)
The HS clinical presentation ranges from what?
mild to severe anemia and can be fatal
What is HS caused by?
By mutation in genes for the erythrocyte membrane skeleton of red blood cells
Dominantly inherited
Describe the erythrocyte membrane skeleton (EMS)
EMS:
Cytoskeleton structure is made up of spectrin
–Long chain; alpha and beta subunits
–heterodimers->heterotetramers
–connected to membrane by ankyrin (anchor symbol)
Why is the structure of EMS important?
Confers property of durability and stability to RBCs
.5 million passages in circulation and tight capillary spaces can beat up a erythrocyte so it needs to be durable and stable to last in the blood for 120 days
What is the most common hereditary anemia ini people of Northern European Descent?
Hereditary Spheryocytosis 1/2000
Have most of the genes for HS been identified?
Yes
What EMS mutation is 63% responsible for HS?
Spectrin/ankyrin defect
What EMS mutation is the cause of 22% of HS cases?
Band 3 defect
What EMS mutation is responsible for 3% of HS cases?
what is responsible for 2%?
Protein 4.2 defect
2%-other defects
What is the percentage of patients that have no known defect for HS?
10%
Dr. Whites rant: This should be disturbing. Very common genetic disease and 1 out of 10 patients we have no idea why they have it
What can the cause of HS of the 10% group of unknown defect possibly be?
A mutation in zing finger protein gene Klf1 (Kruppel-like factor 1)
The Klf1 gene has how many exons and encodes what?
3 exons and encodes 3 zinc finger domains
What does Klf1 zinc finger protein bind to?
Binds to promotoers of all genes in EMS-it turns them on
The mutation for gene Klf1 can be found where? What is defective
A single nucleotide change of GAA to GAT. This changed the Glu to Asp in exon 3: zinc finger domain 2)
A whole CH2 group is missing
defective: makes less RNA from target promotor
The Klf1 mutation is unique to HS how?
It is not found in any other life form with Klf1 protein - only HS carried nucleotide change
Where is the Klf1 DNA binding motif?
RER (Arg-Glu-Arg) DNA binding motif conserved in Klf1 from C. elegans to man
What does RER bind to?
CAACC DNA recognition sequence
What is the mutant form of RER?
RDR
Arg-Asp-Arg
In a normal Klf1, what does R (Arg) interact with?
E (Glu acid) in RER to stabilize interaction with C in the major groove of the CACCC recognition site
In HS Klf1 mutation what does the D (Asp acid) in RDR mutants alter?
The interaction of Arg with E (Glu acid)
Now D in the 2nd Zn finger interacts with the G nucleotide of the opposite strand rahter than the C so DNA cannot unwind - no transcription can then occur
Explain Gel mobility shift assay or EMSA: electrophoretic mobility shift assay
Use: take DNA and see what proteins bind to target promotor regions
Mix radioactive DNA fragment with protein extract from cell
Run electrophoretic gel
See shift of radioactive band when protein is bound to DNA
Depending on size of Protein attached will determine the distance the DNA will travel. The smaller the further it goes
What is affinity chromatography?
Use: isolate DNA binding protein; purification of sequence specific binding proteins
Step 1: Find binding proteins
Have a column with matrix containing DNA of many different sequences
Add low-salt wash to remove proteins that dont bind
Use medium-salt wash to remove binding proteins
Step 2: find specific binding protein
Column with matrix only containing specific DNA sequences
Medium salt wash to remove those not specific to sequences
High salt wash elutes rare protein that specifically binds
What does CHIP: Chromatin Immuno Precipitation allow?
This technique allows identification of the sites in the genome that a regulatory protein binds
-done in living cells
This helps find the specific sequence a known binding protein will bind to.
Uses formaldehyde to glue protein to sequence
Lyse cells
Break DNA into small fragments
Precipitate using Antibodies against protein
PCR product at end can be used to screen a microarray gene chip
What is the DNA region involved in regulating and initiating transcription of a gene?
Gene control region
What does a gene control region include?
Promoter: where transcription factors and RNA polymerase II assembles
&
Regulatory sequences to which regulatory proteins bind to controll rate of assembly process at the promoter
Out of the 25,000 human genes,, how many encode gene regulatory proteins ?
8% or 2,000 genes
What is the encode project?
Figure out: What does the genome do
Exceedingly complex network of controls governing the expression of mammalian genes
What are a few generalities that can be mentioned about the Gene control region?
RNA polymerase and general transcription factors assemble at the promoter
Other gene regulatory proteins (activators or repressors) bind to regulatory sequences which can be adjacent, far upstream or in introns downstream of the promoter
What do gene activator proteins modify?
Local chromatin structure
What favor transcription initiation by increasing accessibility of DNA to other proteins?
Nucleosomes remodeling and histone removal
What are some proteins involved in modifying local chromatin structure?
Chromatin remodeling complex-nucleosomes looser
Histone chaperone protein-remove nucleosome structure
Histone chaperone-allows DNA to relax
Histone-modifying enzyme-histone acetylation allows easier removal of histones
What is the order of events leading to transcription initiation of specific gene?
Gene activator protein binds to chromatin + chromatin remodeling complex
Chromatin is remodeled
Then histone modification enzymes covalently modify histones
The other activator proteins bind to gene reg region
Next, mediator, general transcription factors, and RNA poly assemble the pre-initiation complex at the promotor
Transcription!
Regulatory proteins include gene repressors. What is their role?
Inhibit transcription in different ways
1. activator and repressor compete for same binding site
- Both proteins bind to DNA but the repressor binds to the activation domain of the activator protein
- The repressor binds to DNA and blocks assembly of general transcription factors (direct interactions with general TF)
- The repressor recruits a chromatin remodeling complex which returns the promoter to the pre-transcriptional nucleosome state
- Repressor attracts a histone deacetylase to the promotor - harder to remove deacetylated histones
- Repressor attracts a histone methyl transferase - methylated histones bound to proteins which act to maintain chromatin in silent form
Depending on their composition, the gene regulatory proteins assembled into complexes on DNA can be either what?
Activating or repressing (they are schizophrenic)
The same protein can be part of an activating or repressing complex.
Regulation by “committee”
How are gene regulatory proteins controlled?
- synthesis - make them or not
- Ligand binding - that can make the DNA reg protein but needs a ligand
- Covalent modification-phosphorylation
- Addition of subunit
- Unmasking-use an inhibitor that is removed by phosphorylation
- Nuclear entry - inhibitory protein that does not allow passage
- Proteolysis - released from membrane - cut and free to do as it pleases
What are the alpha-like chains of the globin genes?
Zeta and alpha
What are the beta-like chains of globin chains?
epsilon
gamma
delta
beta
What is the order of hemoglobin switching from embryo-> adult?
How does this process happen?
Embryonic Hb = zeta and epsilon
Fetal = alpha and gamma
Adult = alpha and beta
-not fully clear how hemoglobin switching occurs - lots of research being done to understand
Sickle cells disease. Fetal globin can be used to replace the sickle cell human Hb. Be a cure.
What is interesting about the expression of globin genes during human development?
Globin genes are arranged in linear fashion
Ordered in the 5’ to 3’ direction in the same sequence of activation and expression during embryonic, fetal, and adult development
How big is the region containing five globin genes and locus control region (LCR)?
100kb
Where is the LCR for globin genes? What binds to it?
Far upstream in sequence but required for transcription
Regulatory proteins bind to LCR
The understanding of globin gene regulation may allow what?
The induction of fetal hemoglobin in sickle cell anemia
