Control of Gene Expression 2: Post-Transcriptional Control Flashcards
What are the types of alternative RNA processing?
Optional exon: not all exons are needed to be used.
Optional intron: In some cases, leave the intron in
Mutually exclusive exons: Use one exon or the other
Internal splice site: sometimes the region acts as a true intron and gets spliced out and sometimes part of it is kept in.
What can produce different forms of proteins from the same gene?
Alternative splicing
Splice RNA transcripts differently
____% of genes in humans undergo alternative RNA processing
75
RNA splicing can be regulated negatively by a _______ molecule that prevents splicing machinery access to splice site
Repressor
** Negative control-primary transcript will go on with splicing if no repressor is present
RNA splicing can be regulated positively by activating a molecule that does what?
Recruits and helps direct splicing machinery
**Positive control: primary transcript will not go on to splice unless an activator is present
How do mRNAs leave nucleus?
Through pores
How do mRNAs travel to destination?
Use cytoskeletal motors, random movement, and random movement + degeneration (RNA not trapped is degrade)
What are anchor proteins?
Proteins that hold mRNA in place and when acted on by ribosomes, proteins can be made in the area
This is a way we can control protein expression, gene expression because we localized rna where proteins are needed.
What confers stability of a mRNA?
poly-A tail
Gradual shortening of poly-A tail is done by what enzyme?
exonuclease
What does the shortening of poly-A tail act as?
a timer
Once poly-A tail is reduced to 25 nucleotides, what happens?
Two pathways converge to degrade mRNA
What is the half life of globin mRNA?
10 hours
what is the half life of most mRNAs?
30 min
When mRNA poly-A tail is down to 25 nucelotides, what happens to the 5’ cap and the rest of the poly-A tail?
Decapping: exposed mRNA degraded from 5’ end
** the cap serves to protect RNA from RNA degrading enzymes
mRNA degraded from 3’ end through poly-A tail and into coding region
mRNA regulation by repression of translation and RNA degradation can be seen in what?
What does it involve?
Iron metabolism
Involves iron responsive elements (IREs) and IRP (iron responsive regulatory protein)
Iron transport from intestine to bone marrow involves what?
many proteins that have been recently discovered
Transferrin
What will help bring iron into a cell that needs it?
Transferring receptors
Transferrin-mediated endocytosis
Erythroid precursors in bone marrow have how many TfRs per cell?
800,000
What causes the transferrin receptors to let go of iron in the endosome?
The H ATPase pumps hydrogen into the endosome causing the pH to be 5.5. This acidic environment makes the TfR let go.
However at this pH the transferring can keep hold of the iron and return to the membrane and at 7.2 pH the transferrin receptor will let go and this give a chance for the iron to bind again. This is a cyclic process
What is the iron cycle?
Iron enters the gut lumen-> intestinal absorbtion-> plasma transferrin iron-> marrow erythroid precursors in bone marrow (TfR) -> Circulating erythrocytes->old and taken up by macrophages->plasma transferring iron
Iron can be stored in liver as ferritin
Describe ferritin
Intracellular protein
Binds thousands of Fe3+/molecule
Found in most cells
If you obtain enough ferritin then they make up what?
Hemosiderin: granules of ferritin
Where is excess iron mainly stored by?
Liver, lung, pancreas
If cells are in iron starvation the what must happen?
Cells dont need to store iron and so there is a decrease of ferritin mRNA
Must transport iron into cells
Make more transferring receptor (TfR) mRNA
If there is iron excess what needs to happen?
Excess needs to be stored and transport less iron into cells
So more ferritin mRNA and less TfR mRNA
During iron starvation, what binds to ferritin mRNA that causes no ferritin to be made?
Cytosolic aconitase: an IRP (iron responsive regulatory protein)
It binds to the 5’ ferritin mRNA
During iron starvation, IRP bound to 3’ transferring receptor mRNA causes what?
transferrin receptor to be made, this protects the poly - a tail from degradation
Aconitase
What alters the aconitase 3D shape that causes it to fall off?
Excess iron molecules
Ferritin made
No transferrin receptor made
What are microRNAs?
Regulatory RNAs that regulate messenger RNAs
Noncoding RNAs; 22 nucleotides long - that silence expression of specific mRNA targets
End up degrading RNA or block translation
What do miRNAs bind to?
Complementary sequence in the 3’ UT end of mRNA
Describe the maturation of microRNAs?
again, micro RNAs are repressors of gene activity
Originate as 100 nucleotide precursors
Made as primary miRNA: pri-miRNA - RNA with hairpin loop
Cut down in size to pre-miRNA
Then processed further to mature miRNA
Precursor miRNA is cropped where?
In the nucleus
What does the cropped precursor miRNA form?
Double stranded loop structure
What is precursor miRNA further cleaved by?
Dicer enzyme
Once cleaved by dicer enzyme, what does the miRNA join with?
Argonaute and other proteins to form RISC: RNA-induced silencing complex
**this complex base pairs with mRNA and cleaves RNA: shuts down expression
How many miRNAs are in the genome?
800 to 1,000 and occurs in clusters
A miRNA can regulate ________ mRNA
more than 1
*it can repress hundreds of mRNAs
miRNAs may target ___% of mammalian genes
60
miRNA binding sites are _______.
Widespread
___ miRNA can effect a whole biological program
1
miRNAs can change what in disease states?
Their expression profile
Certain miRNAs can be _______ in stroke or cardiovascular disease
elevated
Circulating levels of miRNA can be used to identify ______.
Cancer
What mi levels are elevated in prostate cancer - this miRNA serves as a biomarker
miR-141
What miRNA is decreased in expression in heart disease?
miR-29
Are changes in microRNA expression causative of disease or responsive to disease?
Yes
Causative: miRNAs likely have mutations that cause disease
Responsive: increased miRNA expression down regulates genes in response to disease to limit severity
Describe Tourette’s syndrome
Neurological disorder manifested by motor and vocal tics
1 in 100
miRNA involvement was found with 1 form of this disease
Variant of SLITRK1 gene shown association
Change in recognition sequence on target SLITRK1 MRNA-> increase miRNA binding
Describe miR-189 involvement with Tourette’s syndrome
It binds more efficiently to target sequence in 3’ UT of SLITRK1 gene and decreases SLITRK1 expression and leads to the disease
Gene has changed and the miRNA recognizes it a little more
What helps proteins to fold appropriately?
molecular chaperonoes; also can bind to co-factors
What is required by proteins to be functional?
Post translation modifications and it must fold into 3D conformations
Describe what can happen to proteins post translation
Modified by protein kinases
Glycosylated
bond to other protein partners
other enzymes modify protein
Thrombin cuts fibrinogen to form fibrin in blood clotting is an example of what?
Protein regulation by post translational processing and modifications
Many molecular chaperones are what?
HSP
HSPs are synthesized in dramatic amounts when? And why?
Temperature is raised to 37 C to 42 C
Increase in temperature leads to increase in misfolding of proteins, there is feedback to synthesize chaperones (HSP) to help proteins refold
What are the two major families of HSP?
HSP 60 and 70
We can control protein activity by choosing what?
What proteins are around
What is an apparatus that destroys aberrant proteins?
Proteasomes
Proteasome accounts for __% of cell protein
1
Proteins selected for destruction binds to what?
Cap area of proteasome which acts as a gate for proteasome
What removes unfolded or abnormal proteins?
Ubiquitin
What does ubiquitin at as?
A recognition tag - identifies proteins to destroy
how many amino acids make up ubiquitin?
76 aa’s
What starts off the ubiquitin process?
E1ubiquitin activating enzyme
Ubiquitin links to _____ ____ chain of E1 enzyme
cysteine side
Once ubiquitin is linked to E1, then it is transferred to what?
E2 ubiquitin ligase (with accessory protein E3), this complex is now primed to destroy proteins
Protein to be degraded has degradation signal that binds to ubiquitin ligase. what is added to the lysine side chain on the target protein?
First ubiquitin chain
What is each successive ubiquitin added to what?
Lysine of ubiquitin chain
What is recognized by proteasome?
Targeted ubiquitin chain on target protein
The specificity of protein degradation proteins: there is one E1 and 1 proteasome but how many E2 and E3 proteins?
30 E2 ubiquitin conjugating enzymes and hundreds of E3 accessory proteins
How is degradation signal on protein activated?
by phosphorylation by protein kinase
Unmasking by protein dissociation
or creating of destabilizing N-terminus
Describe coordinated gene expression
Genes working together, they are not isolated
Expression of critical regulatory protein can trigger batter of downstream genes
Coordinated gene expression in response to need
Describe decision for specialization
Combination of gene control can produce many types of cells.
There are decisions at each steps and results in several different cell types
What is an example of decision for specialization ?
Blood cells: hematopoiesis
What is an example of coordinated gene expression?
Glucocorticoid cortisol
Describe DNA methylation
Represses gene expression.
DNA can be regulated by proteins
DNA itself can be covalently modified
Describe inheritance of DNA methylation
Methylation of cytosine occurs at CG sequences
Cytosine is methylated by “maintenance methyltransferase”
DNA methylation of parent strand serves as template for daughter
Describe genomic imprinting
Based on DNA methylation
Expression of some genes depends on whether genes are inherited from mother or father (maternal is active but paternal silent)
Differential expression of genetic material depending on the parent of origin
Describe epigenetics
Regulation of expression of gene activity without altering gene structure
Describe Prader Willi syndrome
Caused by paternal deletion on chromosome 15 in the region 15q11-q13
PWS subjecct inherits gene deletion from father
PWS has unusual presentation
Genomic imprinting disorders
What are the symptoms of PWS?
Stage one: infatile hypotonia; poor suck; feeding difficulties - failure to thrive
Stage two: hyperphagia (uncontrollable eating); onset of early childhood obesity
Describe obesity in PWS
Obesity is a cardinal feature and most significant health problem
Hyperphagia is the major cause
Average age of onset by 2 years; range 1-6 years may occur as early as 6 months.
Greater than 40% body fat; or 2-3 times higher than in general population
What are the features of PWS
Hypogonadism
Short stature; small hands and feet; hypopigmentation
Mental deficiency; behavioral problems (OCD)
Why does PWS happen?
Paternal gene expression: genes in this chromosomal region is not expressed when inherited from mom but expressed when inherited from dad
Paternal genes are not expressed bc they are deleted and maternal genes remain not expressed even though present
Result: paternal deletion is lack of gene expression due to genomic imprinting
Humans cannot deal well with extra segments of chromosomes or extra chromosomes, so how is XX dealt with?
Dosage compensation occurs so equal # of genes expressed from X chromosome is equal in males and females
One X is inactivated randomly and creates a Barr body
Females are mosaics
Inactivation is maintained post cell divisions: daughter cells maintain XIC - where inactivation starts and spreads
KIC makes XIST RNA - coats entire X chromosome
