RNAP II transcription, TFs, and termination

Question 1

regulatory proteins are ____-specific

Answer 1

tissue-specific

Question 2

regulatory proteins dictate ____ ___ of ____ _____

Answer 2

tissue specificity of cis elements

Question 3

summary of modular nature of RNAPII promoters

Answer 3

• many have a TATA box as a core element (most that don’t, instead have initiator seq or GC islands)
• proximal elements: needed for developmental, env, tissue expression
• promoters that respond to same conditions (but control exp of diff genes) have same cis elements but may be in diff locations relative transcription start site
• enhancer: sometimes composed of multiple binding sites for diff regulatory proteins; combination of trans factors lead to increased transcription initiation

OUTCOME: expression of one gene can be induced/repressed/increased/decreased due to promoter

Question 4

2 roles of TFIID (transcription factor 2 D)

Answer 4

foundation for transcriptional complex
- TFIID - TBP must be bound for transcription to start

prevention of nucleosome stabilization; nucleosome destabilization in promoter region (antagonist to H1)

Question 5

TBP

Answer 5

• highly conserved
• monomer that forms a saddle shape and interacts w minor groove and bends it
• a component of positioning factor (no matter which RNAP is transcribing) -> allows each type of pol to bind to its promoter

Question 6

TAFs

Answer 6

TBP associated factors
- determine whether or not TFIID stays at promoter

Question 7

euk transcription steps

Answer 7

• TFIID binds at TATA box via TBP
• once bound, TFIIB can bind:
  – rate-limiting step in transcription of many genes:
  – proximal enhancers to TFIIB
  – monomeric protein
  – developmental regulation
• TFIIB binds to bent DNA opp and adj to TBP
• TFIIB orients RNAP on DNA
  – RNAPII comes into contact w TFIIB near RNA exit site and active site
• TFIIF binds to mediator RNAPII - directs mediator RNAPII to gathered general factors
• CTD tail (unphos) of RNAPII in contact w TFIID
• binding of TFIIE and TFIIH to complex
• TFIIE = DNA-dep ATPase
• TFIIH contains 9 subunits, w helicase and kinase activity
• RNAPII @ promoter; for transcription to occur, RNAPII must be released from promoter
• TFIIH helicase activity unwinds DNA (w energy from TFIIE) and kinase activity phoshporylates CTD tail
• when CTD tail is phos, detaches RNAPII from TFIID and promoter
  -transcription pause released by additional phos of CTD by CDK9
• promoter clearance; mediator and GTFs released
• RNAPII enters elongation phase