gene promoters and regulation in eukaryotes

Question 1

do TATA and TATA-less promoters initiate and proceed in only one or both directions?

Answer 1

initiates and proceeds in one direction

Question 2

do all other promoters (CpG islands) initiate and proceed in only one direction or both?

Answer 2

initiates in both directions. proceeds in only one direction

Question 3

how is RNA polymerase II loaded on the promoters?

Answer 3

by the general transcription factors (GTFs)

Question 4

at the transcription start site (TSS), there is a surge of +50 base pair sequences read per kb due to ______.. what type of promoter could this be an example of?

Answer 4

uni-directional initiation
TATA promoter

Question 5

what percentage of genes in vertebrates do CpG islands occupy? what rate are they transcribed at?

Answer 5

70%
low rate

Question 6

CpG rich DNA contains ____ nucleosomes and are hence ____ to transcribe

Answer 6

less, easier

Question 7

at CpG islands, what position does transcription initiate within the island?

Answer 7

any position (not defined)

Question 8

at the transcription start site (TSS), there is a surge of -250 bp sequences and a surge of +50 bp sequences read per kb due to __________. where does this take place? (what type of promoter)

Answer 8

bi-directional initiation
CpG islands

Question 9

chromatin immunoprecipitation (ChIP) with anti-RNA pol II antibodies shows ______

Answer 9

the binding of RNA pol II to the analyses DNA (uni and bi directional)

Question 10

in the assembly of pre-initiation complex on TATA-containing promoters, promoter elements (like TATA or the initiator) direct ________

Answer 10

direction general transcription factors to bind DNA

Question 11

in the assembly of pre-initiation complex on TATA-containing promoters, what is the job of general transcription factors?

Answer 11

they position RNA pol II at start sites and assist in initiation

Question 12

how does the pre initiation complex (PIC) commence?

Answer 12

by the association of TFIID to the promoter, followed by TFIIB and TFIIA

Question 13

in the pre initiation complex, after RNA polymerase is recruited, what does the non-phosphorylated CTD (carboxy Terminal Domain) of RNA pol II establish contact with?

Answer 13

severals general transcription factors

Question 14

In the pre initiation complex, after TFIIE and TFIIH are recruited, what does TFIIH helices activity do?

Answer 14

facilitates the opening of the double helix of DNA

Question 15

In the pre-initiation complex, what does the TFIIH kinase activity phosphorylate?

Answer 15

the CTD to release RNA polymerase from the promoter

Question 16

After the initial phosphorylation of ______ by ______, two elongation factors _______ associate with _______ and pause it _____ of the initiation site

Answer 16

CTD, TFIIH kinase, NELF and DSIF, RNA pol II, downstream

Question 17

in the transition from initiation to elongation, another kinase _____, phosphorylates ______. RNA pol II is ______ and ______ begins.

Answer 17

CDK9/CycT/PTEFb, CTD and NELF, elongation