Lecture 3: Gene Structure, RNA, Transcription, Splicing and Non-Coding RNA Flashcards
1
Q
What is reverse transcription?
A
RNA ==> DNA
2
Q
What are exons and introns?
A
Exons: part of gene encoded in transcribed RNA
Introns: DNA region between exons
3
Q
Differences between promoter and enhancer?
A
Promoter: on/off switch close to the gene
Enhancer: dimer further away than the promoter
4
Q
Other name for introns?
A
Intervening DNA sequences
5
Q
What is a poly A tail?
A
Adenines added to the 3’ end of mRNa
6
Q
What is 5’ cap?
A
GTP added to the 5’ end of mRNA
7
Q
What does UTR stand for?
A
Untranslated region of RNA
8
Q
Where are UTRs?
A
Around the coding segment of mRNA
9
Q
What are the 6 types of RNA?
A
- mRNA
- rRNA
- tRNA
- snRNA
- snoRNA
- Other noncoding RNA
10
Q
Role of snRNA? What does it stand for?
A
Small nuclear RNA
Complexed with proteins in the nucleus and involved in RNA splicing
11
Q
Role of snoRNA? What does it stand for?
A
Small nucleolar RNA
Used to process and chemically modify rRNA
12
Q
Product and location of RNA Pol I?
A
rRNA
Nucleolus
13
Q
Product and location of RNA Pol II?
A
hnRNA
Nucleoplasm
14
Q
Product and location of RNA Pol III?
A
tRNA
Nucleoplasm
15
Q
3 steps of transcription and description of each?
A
- Initiation (binding of RNA polymerase to template DNA)
- Elongation (As per base-paring rules nucleotides complimentary to the DNA template are added to the growing RNA molecule)
- Termination (the enzyme and RNA is released from DNA template)
16
Q
Does DNA transcription need a primer?
A
NOPE
17
Q
Is RNA polymerase dependent on a primer?
A
NOPE
18
Q
Is DNA polymerase dependent on a primer?
A
YES
19
Q
Direction of transcription?
A
5’ ==> 3’
20
Q
What is hnRNA? What does it stand for?
A
Primary RNA transcript prior to ANY post-transcriptional modifications
Heterogenous RNA
21
Q
RNA splicing 4 steps?
A
- Binding of specific ribonucleoproteins to the donor and acceptor splice sites of an intron
- Two sites are then brought together by other components of the Spliceosome
- The donor site is then cut and the free end of the intron binds to the branch site within the intron to form a lariat structure
- The acceptor site is cleaved, releasing the lariat, and the exons at the two ends are ligated together
22
Q
What is alternative splicing?
A
A single primary transcript (premRNA) can be spliced in more than one pattern to generate multiple, distinct mature mRNAs leading to expression of protein isoforms with different structural and functional properties
23
Q
In what order does RNA splicing occur?
A
In an order determined by the spliceosome in order to keep the RNA single stranded
24
Q
What % of human genes code for more than 2 alternatively spliced isoforms?
A
75%
25
How many different human proteins?
100K
26
5 alternative splicing methods? Explain each. Which is most common?
1. Exon skipping: an exon may be spliced out of the primary transcript or retained. This is the most common mode in mammalian pre-mRNAs.
2. Mutually exclusive exons: One of two exons is retained in mRNAs after splicing, but not both.
3. Alternative donor site: An alternative 5' splice junction (donor site) is used, changing the 3' boundary of the upstream exon.
4. Alternative acceptor site: An alternative 3' splice junction (acceptor site) is used, changing the 5' boundary of the downstream exon.
5. Intron retention: A sequence may be spliced out as an intron or simply retained. This is distinguished from exon skipping because the retained sequence is not flanked by introns.
27
What gene mutation causes spinal muscular atrophy? What does it code for?
Mutation in SMN1 gene, which codes for the survival motor neuron (SMN) protein
28
What is spinal muscular atrophy?
Second most common recessive human disoder and most common inherited cause of infant mortality
29
Pathway leading the spinal muscular atrophy?
Mutation in SMN1 leading to loss of function ==> SMN2 (the backup gene) contains a silent C>T mutation in the 6th nucleotide on exon 7 ==> exon 7 skipping ==> ineffective SMN2 protein production ==> SMN2 cannot compensate for SMN1 loss of function ==> SMN required for small nuclear ribonucleoproteins (snRNPs), which are important for pre-mRNA splicing ==> loss of function leads to motor neuron degeneration particularly in the spinal cord
30
How does alternative splicing relate to cancer? Example?
Aberrant alternative splicing is common in cancer related genes
A high proportion of DNA variants of BRCA1 and BRCA2 is associated with aberrant splicing in breast/ovarian cancer patients
31
Which gene is most commonly mutated in human cancers?
Tumor suppressor p53
32
p53 nickname? Why?
""the guardian of the genome"" because of its role in conserving stability by preventing genome mutation
33
How does aberrant alternative splicing of p53 work?
Mutations in splice junctions alter the expression of p53 isoforms and can affect splicing through the formation of cryptic splice sites in, for example the middle of an exon
34
What is a cryptic splice site?
A randomly occurring site in the genome that contains a consensus sequence for 5′ or 3′ intron splicing but is not normally used for that purpose, until mutated
35
What is Hutchinson-Gilford progeria syndrome? Symptoms?
Rare but well known entity characterized by extreme short stature, low body weight, early loss of hair, lipodystrophy, scleroderma, decreased joint mobility, osteolysis, and facial features that resemble aged persons
36
Pathway for HGPS?
At least 20 distinct mutations in the prelamina A (LMNA) gene have been linked to HGPS, however the most frequent is a C>T point mutation ==> activates a cryptic splice site donor ==> production of a mutant prelamin A protein, progerin, with an internal 50 amino acid deletion lacking the RSYLLG cleavage site but not affecting the C-terminal ==> CaaX motif where progerin remains permanently farnesylated and carboxymethylated ==> Issues with nuclear envelop strength, shape, and pores (essential for DNA replication and transcription) in SOME cells (not brain cells)
37
Describe HIV.
Lentivirus in the retrovirus family which uses RNA as its genome, causing acquired immunodeficiency syndrome (AIDS) in humans
38
7 steps of HIV replication cycle?
1. Fusion of the HIV cell (capsid protein) to the host cell surface receptors
2. HIV RNA, reverse transcriptase, integrase and other viral proteins enter the host cell
3. Viral DNA is formed by reverse transcription
4. Viral DNA is transported across the nucleus and integrates into the host DNA
5. New viral RNA is used as genomic RNA and to make viral proteins
6. New viral RNA and proteins move to the cell surface and a new, immature, HIV virus forms
7. The virus matures by protease releasing individual HIV proteins
39
How does the X chromosome get inactived in women?
Xist is a non coding RNA gene on the X chromosome of placental mammals that acts as major effector of the X inactivation process via methylation and deacetylation
40
What are miRNAs? How do they work?
Short ~22 nucleotide that encode non-coding RNAs that help regulate gene expression, particularly during development
They function as post-transcriptional regulators. Upon incorporation into the RISC complex, composed of argonaute and associated proteins, the miRNA ‘guide’ strand binds the target mRNA sequences with partial complimentarity (they can have multiple mRNA targets), leading to translation inhibition or mRNA degradation
41
What are siRNAs? What are they used for?
Double-stranded small interfering RNA molecules, 20-25 nucleotides in length that can be chemically synthesized and are being used in therapeutic gene silencing
42
Describe the synthesis of miRNAs.
1. Transcribed by RNA polymerase II (or III) producing long (1000 nucleotides, nt) primary transcripts (primiRs) that like mRNA molecules possess a 5′ cap and a polyA tail
2. The transcripts are processed in the nucleus by the Drosha complex to generate a hairpin-like pre-miRNA precursor, ∼70 nt
3. Exported to the cytoplasm by exportin 5, Dicer degrades the pre-miRNA into the mature ∼19–23 nt miRNA molecule
43
In what diseases are miRNAs the culprits?
Neurodegenerative diseases: Parkinson's, Alzheimer's, and Huntington's
Heart diseases: Cardiac stress and hypertrophy
Diabetes: Pancreatic maintenance and development, Modulators of β-cell function
Carcinogenesis: Abnormal expression of miRNAs in cancer, Deletion of miRNA genes in leukemia, miRNAs as biomarkers of human ovarian carcinoma (OVCA)
44
Potential cause of Alzheimer's?
Protease cleaves APP protein and the cleaved off polypeptides form extracellular plaques
miRNAs usually down-regulate APP and protease levels, but in Alzheimer's miRNA levels are reduced
45
What is a knockout mouse?
Genetically engineered mouse in which one or more genes have been turned off through a gene knockout
46
How do you produce a knockout mouse?
1. Grow pluripotent cells in culture
2. Modify/add gene at that point and inject into blastocyst
3. Inject DNA directly into pronucleus and have randomly incorporated into genome via homologous recombination
4. Then mate chimera and normal to eventually get heterozygous mouse in G2 which can then breed to get homozygous mouse with gene knockout
47
What is a transgenic animal?
Animal that overexpresses a gene
48
What does CRISPR stand for?
Clustered Regularly Interspaced Short Palindromic Repeats
49
How does CRISPR work? Where does this come from?
Cas-9 nuclease with guide RNA to make dsDNA double strand breaks and donor DNA will be inserted via nonhomologous end joining at that locus OR dCas-9 with guide RNA activates or represses certain genes
This system is essential in bacteria immunity, where the guide RNAs are stored from organisms who invade them
50
What is gene drive?
Genetic engineering using CRISPR and Cas-9 that greatly increase the odds that an allele will be passed on to offspring. This can allow it to spread to all members of a population even if they reduce the chance that each individual organism will reproduce
51
What could gene drives do?
1. Immunize animals that carry human disease
2. Control insect-borne diseases
3. Spread pest-specific pesticides and herbicides
4. Reduce populations of rodents and other pests
5. Control invasive species
6. Aid threatened species
52
What are the 5 types of circular RNA?
1. Circular RNA genomes (viroids, hepatitis delta)
2. Excised Intron-derived circular RNA
3. Circular RNA processing intermediates
4. Circular RNA spliced exons
5. Circular, noncoding RNAs in archaea with snRNP functions
53
Potential function of ciRNAs? Where are they found?
Modulate RNA polymerase II in cis and thereby alter the expression of their gene and/or might be miRNA sponges. Consistent with this idea, ciRNAs accumulate in the nucleus and can be localized to their sites of transcription.
