Lecture 13 - Alternative splicing Flashcards

1
Q

why is pol II particular

A

because of the CTD tail

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2
Q

When can you recruit spliceosome parts

A

as soon as the 5’ end of the mRNA transcript is out of pol II

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3
Q

Enzymatic activity associated to CTD tail is ______________ dependent. What are the 3 types of enzymes recruited.

A

phosphorylation. Capping factors. Poly(A) factors. Splicing factors

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4
Q

Why alternative splicing is advantageous and how

A

More exons shuffling and few gene mutants. Since alternative splicing happens with most genes, less DNA is required (less DNA to replicate, maintain, etc.)

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5
Q

Alternative splicing is all about __________ splice sites. How does it do that/principle ?

A

defining splice site. RNA binding proteins (with rna binding motifs) promote or block recognition of a splice site by components of the spliceosome.

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6
Q

Exemple of alternative splicing

A

Fibroblast fibronectin mRNA contains EIIIB and EIIIA part of the fibronectin gene whereas hepatocyte fibronectin doesn’t contain EIIIA and EIIIB part of the fibronectin gene.

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7
Q

In figure with the fibronectin gene, what does each colour and each square correspond to ?

A

each square is an exon. each color is a biochemical particularity that will be obtained in the protein.

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8
Q

what is the advantage of shuffling exons

A

each exon is a particular function in the protein so shuffling them creates a diversity of proteins with different functions

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9
Q

Are all exons spliced ? explain

A

No. You can have exons that are not spliced w/ other exons and that go out w/ introns.

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10
Q

What proteins help define true splice sites

A

SR (Ser-Arg) rich proteins that bind to exonic splicing enhancers (ESE -> sequences in exons) … bind with their motifs.

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11
Q

Alternative splicing controls ____________ in Drosophila. How does it work ?

A

sex determination. Genes in X and Y chromosomes recruit different splicing factors -> different proteins -> sexually dimorphic characteristics

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12
Q

Because females in drosophila have 2 __________, __________ gene is expressed only in ______ in early ____________. 2 __________ = activation of ______________. _____ gene is under ___________.

A

X chromosomes, sex-lethal (Sxl), females, early embryogenesis, X chromosomes. early promoter. Sxl gene is under transcriptional control

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13
Q

What happens later in development concerning promoters of Sxl gene in female drosophila

A

Early promoter is repressed and different Sxl promoter is activated IN BOTH SEXES

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14
Q

Why there is a difference in late Sxl expression in male and female drosophila

A

Sxl pre-mRNA is alternatively spliced depending upon PRESENCE OF SXL PROTEIN. (already present in females !)

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15
Q

Sxl gene (exons) in drosophila. Particularity of one of them

A

3 exons. From 5’ to 3’ : exon 2, exon 3, exon 4. Exon 3 has a premature termination codon.

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16
Q

Sxl protein in females and males

A

F: exons 2 and 4. –> functional protein.
M: exons 2,3,4. Because exon 3 has premature terminating codon, no functional sxl protein is obtained (no sxl prot. in males)

17
Q

How does sxl protein (exists in females only) regulate splicing ? First step

A

Binds to sequence at 3’ end of intron between exons 2 and 3 and blocks association of U2AF and U2 snRNP. (Thus Sxl represses a particular splice site)

18
Q

How does sxl protein (exists in females only) regulate splicing ? Second step

A

U1 snRNP binds properly to 5’ end of intron between exons 2-3 and assembles spliceosome with U2 snRNP that is bound to branch point at the 3’ end of intron between exons 3-4.

19
Q

How does Sxl protein (exists in females only) regulate splicing ? 3rd step

A

Exon 2 is spliced to exon 4. Exon 3 goes out as part of a larger intron.

20
Q

Transfromer gene (Tra) in drosophila (exons). Particularity of one of them

A

3 exons : From 5’ to 3’ : Exon 1, exon 2, exon 3. Exon 2 has a premature terminating codon.

21
Q

Transformer protein in male and female drosophila

A

F : exons 1 and 3

M: exons 1,2,3 -> no functional protein because exon 2 has premature terminating codon.

22
Q

How does Sxl protein regulate splicing in Tra gene. (in females)

A

Blocks splicing at 3’ end of intron between exons 1,2. (blocks binding of U2AF w/ U2 snRNP) so spliceosome formed between splice site at 3’ end of exon 1 and 5’ end of exon 3

23
Q

which protein stimulates dimorphicity in drosophila and what proteins regulate that (only ______ have _______gene)

A

Dsx protein. Tra protein + Tra2 and Rbp1 (SR rich proteins) regulate that. only females have transformer gene

24
Q

Dsx gene (exons) and particularities

A

from 5’ to 3’ : 1,2,3,4,5,6. Exons 4 and 6 have a Poly(A) signal at their 3’ end

25
Q

Spliced exons of dsx gene in males and females and where cleavage and polyadenylation occurs

A

M: exons 3 and 5. cleavage and Poly(A) occur downstream of exon 6.
F: exons 3 and 4. cleavage and Poly(A) occur at 3’ end of exon 4.

26
Q

How does Tra regulate splicing of dsx gene in females ?

A

Rbp1 and Tra2 (SR rich prots) bind to exonic splicing enhancers (ESE) on exon 4 and activate splice site at 3’ end of intron between exons 3 and 4. (recruits U2AF and U2 snRNP to this splice site)

27
Q

Dsx is a ___________________ (what kind of protein). Different _______ are produced in _______ and _________ embryos

A

transcriptional repressor. forms. male. female. embryos.

28
Q

what do we call the different forms proteins that come from same gene (but that are variants)

A

isoforms

29
Q

chicken cochlea (organ that produces nerve impulses in response to sound vibrations) form and description.

A

5 mm long tube that contains epithelium of auditory cells hair cells. Apical hair cell (left of image/goes to the bottom) responds to 50 Hz frequencies and Basal hair cell (right of image/goes to the top) responds to 5000 Hz frequencies.

30
Q

What is the channel in epithelial cells of chicken cochlea that respond to different frequencies. What it is made of

A

Ca 2+ activated K+ channel. 7 transmembrane helices (S0 to S6) that form K+ channel and 4 hydrophobic regions in the cytosol that regulate opening of channel; in response to Ca 2+.

31
Q

How does the chicken cochlea produce auditory hair cells (endothelium of cochlea) that respond to different frequencies

A

By alternative splicing of the Ca 2+ activated K+ channel mRNA primary transcript, isoforms of the channel are produced. These OPEN AT DIFFERENT Ca 2+ CONCENTRATIONS so respond to different frequencies.

32
Q

what is contained by each mRNA of the Dscam gene in drosophila

A

One of the 12 Ig2 exons, One of the 48 Ig3 exons, one of the 33 Ig7 exons and one of the two transmembrane exons.

33
Q

In Dscam protein, what is the region that contains the Ig2, Ig3 and Ig7 exons

A

Homophilic binding region (region that binds to antigen)

34
Q

example of consequence of uncorrect splicing junctions and what this shows

A

Neurological disorders (some have link with abnormality in alternative RNA splicing). This shows that splicing is very specific and must be correct.

35
Q

Process that alters sequence of pre-mRNAs and what it consists of

A

RNA editing. Sequence of coding region in pre-mRNA is altered. Usually single base change (C to U)

36
Q

Comparison of edited mRNA with genomic DNA sequence

A

Sequence of the mature mRNA differs from exons encoding it in genomic DNA.

37
Q

Frequency of RNA editing in eukaryotes and when RNA editing happens

A

Rare in eukaryotes. Happens after processing. (AFTER SPLICING)

38
Q

Exemple of RNA editing

A

APOB gene. 1) In liver, no RNA editing and approx. 4500 a.a. of APOB protein are transcribed. (prot is called apoB-100). 2) In intestine, CAA sequence in 26th exon of transcript of APOB gene is edited to UAA (which is a stop codon). Troncated protein is formed (approx. 2100 a.a. it is called apoB-48)