Alternative Splicing

Question 1

How does the spliceosome interact with the transcript?

Answer 1

RNA-RNA bp (H-bonds)

RNA-protein

Question 2

What is the function of introns?

Answer 2

no explicit function but some have become involved in regulation of gene expression

Question 3

What is the origin of introns?

Answer 3

thought to arise from parasitic, self-splicing GII introns

Question 4

Why do introns still persist?

Answer 4

Stuck due to the complicated process of removal in evolved organisms

Question 5

The splice sites are recognized via the formation of the _

Answer 5

commitment complex (E-complex)

Question 6

What is involved in the commitment complex?

Answer 6

binding of U1 & Splicing Factors (SF) to the 5’SS

binding of factors recognizing sequences of the 3’SS region

Question 7

What are SR proteins? how are they involved in splicing?

Answer 7

serine-arginine proteins

bridge the two splicing regions

Question 8

What is intron definition?

Answer 8

Recognition where elements are defined by interactions across the introns

Question 9

What is exon definition?

Answer 9

Splice sites are defined by interactions across the exon

Question 10

What are pseudoexons?

Answer 10

sequences flanked by the proper splicing sites but has no splicing enhancers

Question 11

What are the mechanisms of splicing enhancers?

Answer 11

1. Anchoring proteins to stabilize early components of the spliceosome
2. Anchoring snRNPs to stabilize early snRNP complexes
3. Steric hindrance to block silencer binding to sequences

Question 12

What are the mechanisms of splicing silencers?

Answer 12

1. Direct competition via steric hindrance of repressors blocking spliceosome
2. Zones of exclusion

Question 13

What are the mechanisms of zone of exclusion splicing silencers?

Answer 13

1. Steric hindrance - binding of multiple silencing proteins block factor access
2. Looping - splicing repressors can loop RNA to silence binding
3. Blocking exon definition - splicing repressors can bind to exon silencing elements and prevents interactions across exons

Question 14

SR proteins bind to _

Answer 14

exonic enhancers

Question 15

hnRNP binds to _

Answer 15

exonic silencers

Question 16

RBPs bind to _

Answer 16

intronic splicing enhancers/silencers

Question 17

The Nova Family is a _ factor

Answer 17

RBP

Question 18

When a Nova factor binds to _ and upstream _ inhibits inclusion of alternative exons

Answer 18

exons

upstream introns

Question 19

When a Nova factor binds to downstream introns it _ the inclusion of alternative exons

Answer 19

promotes

Question 20

When a Fox factor binds to upstream introns it _ the inclusion of alternative exons

Answer 20

inhibits

Question 21

When a Fox factor binds to downstream introns it _ the inclusion of alternative exons

Answer 21

promotes

Question 22

Casette exons are what?

Answer 22

exons alternatively left out or included in the final mRNA

Question 23

Exons may be alternatively sized if…

Answer 23

they have alternate splice sites

Question 24

Intron retention is common in _ & _

Answer 24

plants and yeasts

Question 25

The splicing pattern of a gene may be disturbed by _, _ structures may result in skipping

Answer 25

mutations

secondary

Question 26

What effect does alternative splicing have on RPL30 protein gene?

Answer 26

Changes in nuclear concentration by regulating its own splicing and translation (preventing intron splicing)

Question 27

What effect does alternative splicing have on CD44 exclusion in stimulated T-cells?

Answer 27

Ras/MAPK -> phosphorylates SAM68 via ERK ->stimulates the gene to include exon v5 in the CD44 transcript

Question 28

Alternative splicing supposedly played a part in the _ system evolution in vertebrates. Give one example of its influence

Answer 28

nervous

in neurons the N1 exon is included in its transcript but excluded in somatic cells due to PTB looping