Alternative splicing

Question 1

How many protein coding genes are in the human genome

Answer 1

~25,000

Question 2

What % of protein coding genes form multiple isoforms

Answer 2

40%

Question 3

How are protein isoforms formed

Answer 3

Alternative splicing

Question 4

At what stage of RNA processing does alternative splicing occur

Answer 4

Between the RNA transcript and the production of mature RNA (mRNA)

Question 5

Give a detailed physiological example of alternative splicing in development

Answer 5

Neurogenesis where embryonic astrocytes produce SDF1 alpha/beta (stromal derived factor) - ligand for CXCR4 (g-cpupled protein receptor). This enables vascular formation for the deeloping brain.

However in mature atrocytes SDF1 is alternatively spliced to produce a membrane bound SDF1 gamma which has an anti-inflamatory role which protects astrocytes.

Question 6

Why is alternative splicing important

Answer 6

Important as it brings about differential expression between tissues by using the same genome

Question 7

What are exons

Answer 7

Coding parts of the DNA

Question 8

What are introns

Answer 8

Interupting sequences

Question 9

Outline the stages of alternative splicing

Answer 9

1. Original DNA containing introns and exons
2. RNA transcript is produced which contains introns
   and exons
3. RNA transcript then undergoes splicing to produce
   2 mRNA transcripts

Question 10

Give an example of alternative splicing of calcitonin

Answer 10

Calcitonin gene is present in all cells. In the Thyroid it is Important in regulation of blood calcium levels as it surpresses osteoclast funtion and therfore lovers blood calcium.
However in the neuron calcitonin gene is alternatively spliced to produce CGRP = important in vasodilation and pain transmition

Question 11

What is the mechanism of alternative splicing

Answer 11

1. Original DNA containing introns/exons
2. U1 (small nuclear riboprotein) attatches to the 5’ end
   of a exon or intron within the RNA transcript
3. This promotes the celavage from the intron/exon
4. U2AF attatches to the 3’ end of intron/exon
   boundary which joins up all the small nuclear
   riboproteins. This forms a splicosome.
5. This cleaves the introns out from between the
   exons which are then re-attatched.

Question 12

What is a spliceosome

Answer 12

Multiprotein complex which funtions to cleave introns from exons and joins introns together.
Contains SR proteins (serine/arginine rich) and small nuclear riboproteins (snRNP)

Question 13

How is alternative splicing regulated

Answer 13

by cis (intronic) acting regulatory elements (elements within the gene itself) which recruit trans-acting (exonic) splice factors.

Question 14

What is a cis factor

Answer 14

factor that woks WITHIN THE GENE (recruits trans-factor)

Question 15

What is a trans-factor

Answer 15

Factor which is EXTERNAL and is recruited to the gene

Question 16

What is the most common form of splicing factor used to regulate alternative splicing?

Answer 16

SR proteins (serine/arginine rich)

Question 17

How is alternative splicing deregulated in cancer

Answer 17

mutations within the core splicosome componants e.g - snRNPs

• Splicing factors
• Cis regulatory elements

Question 18

What are the effects of mutations in snRNP’s and splicing factors

Answer 18

Global deregulation of mRNA splicing = involved in alternative splicing in the whole genome

Question 19

What are the effects of mutations in Cis regulatory elements

Answer 19

Deregulation of specific mRNA splicing

Question 20

What are the implications for a cacner cell if

alternative splicing is deregulated

Answer 20

1. splicing of proto-oncogenes to produce
   constitutively active variants
2. Splicing of TS’s to produce non-functional variants

Question 21

Give an example of alternative splicing in cancer

Answer 21

amplification of SF1 (SR protein) - causes global deregulation

Question 22

What is SF1

Answer 22

Serine/Arginine rich splicing factor 1