Download Transcription part (10/2/2015)

MCB 2015. Questions for Seminar 4A (Michael)
Transcription part (10/2/2015)
Assignments:
GR1: Q1, Q2, Q10;
GR2: Q3, Q4;
GR3: Q5, Q6, Q18
GR4: Q7, Q8, Q9;
GR5:Q11, Q12, Q19;
GR6+8: Q13, Q14, Q17;
GR7: Q15, Q16
1. At which stage of mRNA synthesis does the cap attachment to pre-mRNA occur?
What is the connection between the CTD phosphorylation and Cap attachment? What is
the CTD and what is special about its sequence? Which initiation factor (TFII)
phosphorylates CTD?
2. What is the signal of nuclear mRNA poly-adenylation? What role does CTD play in
mRNA poly-adenylation? Describe how the poly-adenylation of mRNA is carried out in
the nucleus.
3. Why does CTD become phosphorylated first at Ser 5 and then at Ser2? How is the Ser2
phosphorylation connected with the de-acetylation of histones in the nucleosomes of transcribed
DNA? Describe the roles of Set1, SAGA and Set2, RPD3 in this process. Name kinases that run
the Ser 5 and Ser 2 phosphorylation in CTD (some of them are important for the cell cycle).
4. Eukaryotic promoters often contain elements other than TATA box. How are the Inr
(Initiator) and DPE (Downstream Promoter Element) sequences in promoters
recognized? What is the role of TAFs in this process?
5. What is the role of histone acetylation by HATs? Name at least one protein complex
and one co-activator protein that run the acetylation. How can the histone acetylation
affect the TF binding to the promoter proximal regions?
6. Histone 3 is often methylated in chromatin regions containing non-transcribed genes.
What does this methylation do? Describe the effects of K9 methylation on HP1
promoted gene silencing. What is the role of Suv39 methylated in gene silencing?
7. Methylated Lysines (K-s) in histones are recognized by specific protein domains. What
are the names of those domains? Why does the extent of methylation (mono-, di- and
three-Me) matter?
8. What do ISWI, SWI and SWR1 chromosome re-modeling machines do and what is
the difference between them? Why do SWI machines have bromo-domains?
9. Nucleosome presence will certainly impede RNAPII progression along DNA. How
this problem is taken care of? What is the role of FACT and Spt6 in this process?
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10. You study transcription initiation in vitro using 'naked' DNA (without nucleosomes) that
contains a reporter gene under control of promoter containing CRE proximal element. Would the
phosphorylation of Ser133 in CREB stimulate the transcription ? Would the addition of dephosphorylated CREB stimulate the transcription? Explain why. Assume that all general
transcription factors (including TAFs of TFIID) and CBP/p300 are present.
11. Splicing of exons in pre-mRNA is done by Spliceosome. How does spliceosome
recognize introns in pre-mRNA? What is the role of U1 and U2 particles in this process?
Which end of intron is easier to recognize? Why do we have introns in our genomes?
12. How is the branching A in intron defined during splicing? What are the roles
SF1/BBP and U2AF in this process? Describe their interplay with U2 RNP in the
definition of the 3’ of intron. What is the role of SR proteins in exon definition?
13. What is the role of EJCs (exon junction complexes) in the mRNA transport into the
cytoplasm. Describe the normal transport of mRNA from the nucleus that relies on the
use of Tap/p15 transporter. What is the role of Dbp5 helicase here? How does the
Brownian ratchet work?
14. Rev protein of HIV participates in the transport of HIV mRNAs into the cytoplasm.
HIV virus with a mutant Rev does not form infectious virus particles. Explain why.
Describe also how Rev normally works.
15. Transformer protein (Tra) in Drosophila determines the alternative splicing of Dsx
genes. You find a mutation in the transformer gene that results in the female phenotype
even in the mutants with a disrupted Sxl gene. What kind of mutations in the Tra gene
could have occurred?
16. A researcher introduces a mutation into the AAUAAA sequence in the end of a
gene. She finds that a AAGAAA mutation leads to the production of a much longer
mRNA that is poorly poly-adenylated. Explain this observation.
17. Many TFs are activated by the receptors on the cell surface by a receptor catalyzed
phosphorylation. The phosphorylation often opens NLS (nuclear localization signal) in a
factor sequence that interacts with Importin b. Describe the mechanism of the activated
factor delivery into the nucleoplasm (Ran-cycle). What is the role of GTP hydrolysis in
the Ran cycle?
18. What is the role of Mediator in the activation of transcription by RNAPII? Why does
it leave RNAPII after initiation?
19. P-TEFb protein is important in transcription elongation. What does it do? How does
it remove the block imposed by DSIF and NELF anti-elongation factors?
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