Transcription and regulation

Question 1

What regions define a gene principally?

Answer 1

• Enhancer
• Proximal promoter
• Core promoter
• TSS

Question 2

What is the core promoter comprised of(positions too)?

Answer 2

• CGI(upstream), CpG islands found in 80% of protein genes and housekeeping genes
• BRE(-35), TFIIB recognition element
• TATA box(-25), Only present in 10% of genes
• Initiator(TSS)
• DPE
• They all alter the probability, transcription usually occurs in bursts

Question 3

What polymerase transcribes ncRNA?

Answer 3

• Poll II

- They generally overlap with existing genes in the introns, opposite direction, ect

Question 4

How is the transcription pre-initiation complex(PIC) assembled using GTFs?

Answer 4

1) TFIID +TBE: bind to DPE and link TBE(minor grove) to part of the core promoter
2) TFIIA: stabilizes interaction
3) TFIIB: Bind to BRE and help recruit Polymerase
4) TFIIF + RNA Pol II: Attach t complex with C terminal tail accessible
5) E+H: Attach to Pol. H acts as a helicase, phosphorylates C terminal at every 5th Ser
6) RNA Pol escapes(not release) and leaves PIC behind

Question 5

What is RNA Pol II posing?

Answer 5

• Creates 20bp then stops before first histone
• Usually very transient state, but can be primed for fast response
• DSLF + NELF attach to Pol II
• Both get phosphorylated by PTEFb, NELF gets released
• Every 2nd Ser gets phosphorylated
• This leads to different interaction with the mediator
• Elongation factors are recruited to the tail
• Pol II is released

Question 6

What are the 4 steps of transcription initiation?

Answer 6

1) Assembly of PIC until Ser 5 phosphorylated
2) RNA Pol escape, makes short transcript
3) Posing
4) Release

Question 7

What are the several roles of TFs and what bottleneck do the support?

Answer 7

• Just general TFs too inefficient in vivo
• Bind to promoters and enhancers
• Help assemble PIC
• Stabilize and recruit general TFs
• Mainly TFIID/A/B to deal with early bottleneck
• Attract general TF directly or as coactivators(to mediator)

Question 8

What is the role of the mediator?

Answer 8

• Interacts with TFs bound to enhancers

Question 9

What are the mediator’s two states?

Answer 9

1) Unphosphorylated
- interacts with: GTFs, TFs, non-phosphorylated RNA Pol II
- Starts intitiation by attracting TFIIH which phosphorylated Ser2 tail, then detaches due to (P)-RNA Pol
2) Phosphorylated Mediator
- interacts with elongation factors, superelongation complex(SEC) , pTEFb
- Starts release by attracting pTEF to RNA Pol for release

Question 10

What are the early stages of lambda regulation?

Answer 10

• PL and PR have higher affinity for Pol II

- PL synthesizes N, PR Cro, which are antitermination factors

Question 11

What are the intermediate stages of lambda regulation?

Answer 11

• Further range allows PR to transcribe cII and PL cIII and int
• But cII degraded by proteases in the presence of nutrients
• cIII inhibits proteases
• cII TF for PRE to synthesize cI

Question 12

What are the late stages of lytic lambda regulation?

Answer 12

• cI dominates cro as a TF for PRM
• Dependent on cII not suppressed
• Cro not accumulated enough to suppress cI

Question 13

What are the late stages of lysogenic lambda regulation?

Answer 13

• Cro dominates cI as a Tf for PR

- Dependent on plenty of nutrients and cro accumulation in early stages

Question 14

How do general TFs assemble at promoter?

Answer 14

• TAF polymere TFIID attaches to DPE and core promoter
• TFIIA stabilizes interaction
• TFIIB binds to BRE
• TFIIB and TFIID recruit TFIIF and RNA pol II
• TFIIE/H recruited which phosphorylates Ser at C-terminal