B2.072 RNA Processing and Gene Regulation

Question 1

SMN1

Answer 1

survival of motor neuron 1 protein
interacts with snRNPs
critical for snRNP assembly

Question 2

SMN2

Answer 2

can partially compensate for loss of SMN1
most SMN2 mRNAs have exon 7 spliced out
produces less stable protein

Question 3

what was observed with an experimental SMN1 gene knockout?

Answer 3

widespread pre-mRNA splicing defects
hundreds of diverse transcripts affected
mRNAs from genes with large numbers of introns especially affected

Question 4

why does a defect in SMN1 cause significant neuromuscular problems?

Answer 4

insufficient numbers of snRNPs
weak splice sites utilized less than strong ones > normal ratio of variants altered
proteins do not carry out necessary functions for cells to work normally/live

Question 5

how can a SNP within an intron of a tumor suppressor gene increase cancer risk?

Answer 5

transcriptional or splice elements influenced by the particular SNP
alters expression of splicing

Question 6

what is the overall mechanism of tumor suppressor gene KLF6 and its splice variant KLF6-SV1

Answer 6

KLF6 protein is in nucleus and has tumor suppressor activity (induces cell cycle arrest)
KLF6-SV1 protein in cytosol
binds to KLF6 preventing it from working in the nucleus
no tumor suppressor activity

Question 7

what is beta thalassemia

Answer 7

reduced or absent beta globin (part of hemoglobin complex)

Question 8

what determines the clinical severity of beta thalassemia

Answer 8

extent of imbalance between alpha and beta globin chains

carrier: heterozygous, asymptomatic
intermedia: heterogenous, can be asymptomatic to severe
major: severe transfusion dependent

Question 9

B0 vs B+

Answer 9

B0 = no B chain synthesis
B+ = some B chain synthesis

Question 10

describe the mechanism of a intron 2 acceptor site B0 mutation

Answer 10

mutation kills normal acceptor site
cryptic splice site within intron 2 is used instead
stop codon within retained portion of intron, premature termination and no functional protein

Question 11

describe the mechanism of a intron 1 B+ mutation

Answer 11

creates a new, strong acceptor splice site
both mutant and correct sites used, but mutant used more
retained portion of intron 1 has in frame termination codon

Question 12

describe the mechanism of an exon 1 B+ mutation

Answer 12

creates a new donor splice site in exon 1
both sites used
incorrect splicing produces frameshift mutation, translation terminates at stop codon in exon 2

Question 13

what are 3 ways that SNP/mutation can alter splicing

Answer 13

1. alters splice donor or acceptor (B thal)
2. alters binding of factor that regulates splicing
3. alters machinery needed for splicing to occur

Question 14

what is one way to possibly treat mutations in splicing variations?

Answer 14

AON binding of protein to RNA elements that block inclusion of certain exons in splicing

Question 15

difference between Duchenne and Becker muscular dystrophy

Answer 15

Duchenne- loss of a particular domain that results in tears in muscle cell membranes and eventual lack of function
Becker: splicing defect resulting in reduced number of repeats, but reading frame intact. still functional protein, mild disease

Question 16

Duchennes nonsense mutation

Answer 16

alternative splicing adds a premature stop codon into mRNA

mutant protein is not functional

Question 17

Becker mutation

Answer 17

alternative splicing skips an exon

mutant protein still function