Lecture 3 - transcription in Eukaryotes

Question 1

Compared to bacterial RNA polymerase, how many subunits do eukaryotic RNA polymerases have?

Answer 1

they have 12 core subunits compared to bacterial which only have 5

Question 2

What are focused promoters?

Answer 2

they initiate transcription at a single transcription start site

Question 3

What are dispersed promoters?

Answer 3

they initiate transcription at one of many transcription start sites in a 50-100 nucleotide region, which is common in vertebrate organisms

Question 4

What is the directionality of eukaryotic promoters usually?

Answer 4

bidirectional

Question 5

What is the TATA box?

Answer 5

a binding site for TATA-binding protein
*they are uncommon in vertebrates

Question 6

What does the initiator (Inr) encompass?

Answer 6

the transcription start site

Question 7

Since the initiator complex is highly degenerate (lots of possibilities) in vertebrates, what does this enable?

Answer 7

the use of dispersed core promoters

Question 8

What letter of the initiator is the start site? (YYANWYY)

Answer 8

A

Question 9

What is basal transcription?

Answer 9

when the core promoter produces a low level of transcription

Question 10

Name 2 examples of regulatory elements that are usually positioned near the promoter.

Answer 10

GC and CAAT boxes

Question 11

What do regulatory factors do?

Answer 11

they bind to regulatory elements to activate or repress transcription
*this is a trans-acting mechanism

Question 12

What do enhancers do?

Answer 12

they stimulate transcription over long distances (they are promoters!)

Question 13

What do silencers do?

Answer 13

they inhibit transcription

Question 14

What do enhancers help to do?

Answer 14

recruit RNA polymerase II to a promoter and to help stimulate the transition from transcription initiation to productive elongation

Question 15

What does the Mediator Complex do?

Answer 15

it bridges the gap between gene promoters and enhancers

Question 16

List the general steps of eukaryotic transcription initiation.

Answer 16

Pre-initiation complex (PIC) assembly, open complex formation, transcription start site scanning, promoter escape, promoter-proximal pausing, and pause release and productive elongation

Question 17

What is TFIID and what does it do?

Answer 17

its composed of TATA-binding protein (TBP)
* it recognizes the TATA box and many other core promoter elements (including the initiator)

Question 18

What doe TFIIB do?

Answer 18

it binds to TFIID and helps to recruit RNA polymerase II to the promoter, partially binding to TFIIF

Question 19

What does TFIIF do?

Answer 19

TFIIF binds to RNA polymerase II and helps to mediate recruitment of Polymerase II to they promoter by interacting with TFIIB

Question 20

What does TFIIE do?

Answer 20

recruits TFIIH to the pre-initiation complex and stimulates the helicase and CTD phosphorylation activities of TFIIH

Question 21

What does TFIIH do?

Answer 21

Unwinds DNA to form an open complex using helicase activity and phosphorylates the RNA polymerase II CTD during the transition from initiation to elongation

Question 22

What is the first step in the mechanism of transcription initiation?

Answer 22

the TFIID binds to the TATA box (or other core promoter elements)

Question 23

Step 2 of the mechanism of transcription initiation?

Answer 23

TFIIB binds to TFIID

Question 24

Step 3 of the mechanism of transcription initiation?

Answer 24

TFIIB promotes the binding of RNA polymerase II to the core promoter… here, TFIIF interacts wit TFIIB

Question 25

Step 4 of the mechanism of transcription initiation?

Answer 25

TFIIE and TFIIH binds to RNA polymerase II to form the pre initiation complex

Question 26

Step 5 of the mechanism of transcription initiation?

Answer 26

TFIIH uses its helicase activity to unwind DNA and form an open complex. TFIIH then phosphorylates the RNA polymerase II CTD, which releases Pol II TFIIB and TFIIH are released

Question 27

What occurs during promoter escape?

Answer 27

rna polymerase breaks free of the promoter elements

Question 28

what occurs during promoter-proximal pausing?

Answer 28

RNA polymerase pauses just downstream of the promoter

Question 29

What occurs during the pause release and productive elongation stage?

Answer 29

RNA polymerase exits the pause and transcribes the gene

Question 30

What protein causes pausing?

Answer 30

pausing is induced by Negative Elongation Factor
*NELF restrains RNA polymerase II

Question 31

What is promoter-proximal pausing important for?

Answer 31

*for keeping promoters in an active states
*RNA quality control
*and gene regulation

Question 32

Which protein releases RNA polymerase II from the pause by phosphorylating the CTD?

Answer 32

Positive Transcription Elongatio factor b (P-TEFb)

Question 33

What does CTD phosphorylation coordinate?

Answer 33

the RNA polymerase II transcription cycle

Question 34

Throughout the transcription cycle, CTD becomes what?

Answer 34

highly phosphorylated

Question 35

At the beginning of genes, what is highly phosphorylated?

Answer 35

Ser5

Question 36

What is the phosphorylation of Ser5 involved in?

Answer 36

recruiting capping enzyme

Question 37

What two amino acids are involved in recruiting the spliceosome to mRNA?

Answer 37

Ser5 and Ser2

Question 38

What is the polyadenylation signal sequence required for?

Answer 38

to add poly-A tail to mRNA