Gebelein 2

Question 1

Phosphorylation of ________ of the CTD of RNAPolII is a key step in transcription initiation.

Answer 1

Ser-5

Question 2

The complex that is recruited to promoter sequences to initiate transcription is called the ____________________.

Answer 2

Pre-initiation complex (PIC)

Question 3

The enzyme responsible for phosphorylating the CTD of RNAPolII during transcription initiation is __________.

Answer 3

TFIIH

Question 4

The super elongation complex (SEC) is recruited to the gene after _______________ clearance from the PIC.

Answer 4

RNA PolII

Question 5

The CTD of RNAPolII interacts with the __________, a complex that bridges the enhancer to the promoter.

Answer 5

Mediator

Question 6

Disease-associated SNPs are often located in _________ DNA.

Answer 6

non-coding

Question 7

Enhancers regulate the __________, __________, __________, and __________ of transcription.

Answer 7

rate, quantity, time, place

Question 8

TFs often have multiple regulatory domains that can participate in __________, __________, or both.

Answer 8

activation, repression

Question 9

The DNA binding domain of a TF binds DNA in a ________________ manner.

Answer 9

sequence-specific

Question 10

Two examples of regulatory domains in TFs are ______________________ and ______________________.

Answer 10

Histone acetyltransferases (HATs), Histone deacetylases (HDACs)

Question 11

HATs are histone ______________________ that promote chromatin __________.

Answer 11

Acetyltransferases, opening

Question 12

HDACs are histone ______________________ that promote chromatin __________.

Answer 12

Deacetylases, closing

Question 13

The ATPase that can move nucleosomes to expose additional TF binding sites is called __________.

Answer 13

SWI/SNF

Question 14

______________________ is the mediator that bridges the distant enhancer to the promoter and RNAPolII.

Answer 14

ARC/DRIP/TRAP

Question 15

The Mediator interacts with ______________________ complexes to promote looping.

Answer 15

Cohesion

Question 16

The Mediator is part of the __________ that promotes RNA polymerase initiation via TFIIH.

Answer 16

PIC

Question 17

The Mediator promotes RNA polII __________ by activating the SEC/cdk9/P-TEFb kinase.

Answer 17

elongation

Question 18

______________________ is a transcriptional repressor that recruits an HDAC complex.

Answer 18

Hairy

Question 19

Core promoters contain information necessary to __________ transcription at the proper base-pair.7

Answer 19

initiate

Question 20

______________________ elements and ______________________ contain the information to control the time, place, and amount of transcription.

Answer 20

Promoter-proximal, enhancers

Question 21

Regulatory sequences (CRMs) account for __________ times more of the human genome than exons.

Answer 21

10

Question 22

A typical CRM is __________ bps long and contains binding sites for __________ individual transcription factors.

Answer 22

200, 3-10

Question 23

______________________ footprinting is a useful technique to identify key binding sites in enhancers.

Answer 23

Phylogenetic

Question 24

Different enhancers for different tissues contribute to the __________ of enhancers.

Answer 24

modularity

Question 25

The even-skipped (eve) gene is an example of a gene that uses ______________________ control to achieve specific expression patterns.8

Answer 25

combinatorial

Question 26

The homeodomain is an example of a ______________________.

Answer 26

DNA-binding domain

Question 27

TFs have ______________________ site preferences and can tolerate some non-optimal nucleotides.

Answer 27

binding

Question 28

Critical binding sequences are more likely to be ______________________ than non-critical sites.

Answer 28

conserved

Question 29

GR interacts with co-regulatory proteins like __________, __________, and __________.

Answer 29

SWI/SNF, p300/CBP, ARC/DRIP/TRAP

Question 30

______________________ promoters tend to be accessible, while ______________________ promoters tend to be bound by nucleosomes.

Answer 30

TATA box, TATA minus

Question 31

Paused polymerase is a common phenomenon in ______________________, affecting ~70% of genes.1

Answer 31

Metazoans

Question 32

__________ is a negative elongation factor involved in promoter pausing.

Answer 32

NELF

Question 33

Pause release is mediated by __________, which phosphorylates Ser2 of RNAPolII CTD.

Answer 33

P-TEFb

Question 34

__________ is converted into a positive elongation factor via phosphorylation by P-TEFb.

Answer 34

DSIF

Question 35

Having a gene that is paused allows ______________________ to modulate transcription.1

Answer 35

sequence-specific TFs

Question 36

______________________ assays are used to assess promoter activity in cells.

Answer 36

Reporter

Question 37

Mutations in potential promoter sequences can be analyzed using ______________________ assays to determine their role in promoter activity.

Answer 37

reporter

Question 38

The carboxyl terminal domain (CTD) is part of the __________ subunit.

Answer 38

Rbp1

Question 39

The consensus repeat in the CTD is __________, which contains 5 potential sites of __________.

Answer 39

YSPTSPS, phosphorylation

Question 40

Deletion of more than half of the __________ repeats in the CTD results in lethality in yeast.1

Answer 40

CTD

Question 41

TFIIH subunit (cdk7) phosphorylates __________ in position 5 of the CTD.1

Answer 41

serine

Question 42

Phosphorylation of CTD at Ser5 is essential for __________ and recruitment of factors like the ______________________.

Answer 42

Initiation, mRNA capping machinery

Question 43

The non-phosphorylated form of Pol II is called __________, and it assembles in the __________.

Answer 43

IIA, PIC

Question 44

Phosphorylation of the CTD switches to __________ for Pol II elongation competence.

Answer 44

Ser2

Question 45

P-TEFb stands for ______________________________________________.1

Answer 45

Positive transcription elongation factor

Question 46

CDK9 and P-TEFb are the same and are part of the __________.

Answer 46

SEC

Question 47

TFIIH is involved in RNA polII __________, while SEC/Cdk9/P-TEFb is involved in RNA polII __________.

Answer 47

initiation, elongation

Question 48

Much of the __________ can remain associated with the core promoter after PolII release, potentially contributing to transcriptional bursting.

Answer 48

PIC