GEBELEIN 2

Question 1

The Mediator complex recruits the ________ after PolII clearance from the PIC.

Answer 1

super-elongation complex (SEC)

Question 2

CDK9 and ________ are the same and are part of the SEC.

Answer 2

P-TEFb

Question 3

Much of the _______ can remain associated at the core promoter after PolII release – may contribute to transcriptional bursting!

Answer 3

PIC

Question 4

The processes of RNA polII initiation (TFIIH) and elongation (SEC/Cdk9/P-TEFb) are differentially controlled by ________!

Answer 4

kinases

Question 5

_________ contain information necessary to initiate transcription at the proper base-pair.

Answer 5

Core promoters

Question 6

Other elements contain the information to control time, place, and amount of transcription - These are ________ and _________.

Answer 6

promoter-proximal elements, enhancers

Question 7

These control elements function by recruiting ___________.

Answer 7

sequence-specific TFs

Question 8

________% of the genome is regulatory sequence.

Answer 8

20

Question 9

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

Answer 9

10x

Question 10

Disease-associated SNPs are often located in ___________ (some estimates as high as 95%).

Answer 10

non-coding DNA

Question 11

The phenotype of a Belgian family with autosomal dominant preaxial polydactyly was caused by a mutation within an _________.

Answer 11

enhancer

Question 12

The mutation responsible for autosomal dominant preaxial polydactyly was mapped to a long-range enhancer element within the _________ gene.

Answer 12

Sonic-hedgehog (Shh)

Question 13

Most genes have multiple enhancers. This is known as ________.

Answer 13

Modularity

Question 14

Enhancers can be located _______ of the promoter.

Answer 14

up or downstream

Question 15

Enhancers can be located in ________ regions.

Answer 15

intronic

Question 16

Enhancers can be located varying distances up to _______ away.

Answer 16

1mb

Question 17

Enhancers regulate the _________ of transcription.

Answer 17

rate

Question 18

Enhancers regulate the _______ of transcription.

Answer 18

quantity

Question 19

Enhancers regulate the _______ of transcription.

Answer 19

time

Question 20

Enhancers regulate the _______ of transcription.

Answer 20

place

Question 21

Enhancers typically have binding sites for several different _______ – each of which is required to mediate appropriate output.

Answer 21

TFs

Question 22

Key binding sites in enhancers are more likely to be ________ = utility of phylogenetic footprinting.

Answer 22

conserved

Question 23

Different enhancers for different tissues is an example of ________.

Answer 23

Modularity

Question 24

Separate enhancers and ________ contribute to making stripes in flies.

Answer 24

combinatorial control

Question 25

Different Enhancers of the ________ gene control distinct transcription bands in the embryo.

Answer 25

even-skipped (eve)

Question 26

________ encode ‘instructions’ for gene expression.

Answer 26

Cis-regulatory modules (CRMs)

Question 27

A ‘typical’ CRM is _______ bps.

Answer 27

~200

Question 28

A ‘typical’ CRM has binding sites for ______ individual transcription factors.

Answer 28

~3-10

Question 29

TFs often have multiple regulatory domains that can participate in ______, ______, or ________.

Answer 29

activation, repression, or both

Question 30

The ________ binds DNA in a sequence-specific manner.

Answer 30

DNA binding domain

Question 31

Examples of DNA binding domains include _________.

Answer 31

homeodomain, zinc finger

Question 32

Regulatory domains activate or repress by recruiting _________.

Answer 32

co-regulatory proteins

Question 33

Examples of co-regulatory proteins include ________ such as P300 or _________.

Answer 33

Histone acetyltransferases (HATs), histone deacetylases (HDACs)

Question 34

TFs have _________ and can tolerate some non-optimal nucleotides.

Answer 34

binding site preferences

Question 35

___________ are more likely to be conserved than non-critical sites.

Answer 35

Critical binding sequences

Question 36

Once bound, the TF recruits regulatory proteins that can alter __________ activity in a number of ways.

Answer 36

RNA polII

Question 37

_______ is targeted to the HRE DNA sequence

Answer 37

GR

Question 38

Once bound, GR interacts with multiple co-___________ proteins.

Answer 38

regulatory

Question 39

________ is an ATPase that can move nucleosomes to expose additional TF binding sites.

Answer 39

SWI/SNF

Question 40

_______ is a histone acetyltransferase (HAT) that alters histones to promote chromatin opening.

Answer 40

p300/CBP

Question 41

________ is the Mediator! It bridges the distant enhancer to the promoter and RNAPolII.

Answer 41

ARC/DRIP/TRAP

Question 42

The Mediator interacts with ________ to promote looping.

Answer 42

Cohesion Complexes

Question 43

The Mediator links distant _______ to _________.

Answer 43

enhancers, promoters

Question 44

The Mediator is part of the ________ that can promote RNA polII initiation.

Answer 44

PIC

Question 45

The Mediator can promote RNA polII elongation by activating the _______.

Answer 45

SEC

Question 46

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

Answer 46

preinitiation complex (PIC)

Question 47

Mediator stays at the core promoter after ________ –recruit additional RNA polII which may contribute to transcriptional bursting!

Answer 47

PolII release

Question 48

The Mediator promotes RNA polII elongation by activating the ________ that phosphorylates Ser2 on the RNA polII CTD.

Answer 48

SEC/cdk9/P-TEFb kinase

Question 49

_________ is a transcriptional repressor that recruits an HDAC complex that promotes nucleosome closing and blocks binding.

Answer 49

Hairy

Question 50

Regulatory proteins can have a direct link to _______ to increase PIC loading.

Answer 50

GTFs/RNA polII

Question 51

Regulatory proteins can be multi-functional – link to GTFs/PolII and provide __________.

Answer 51

enzyme activities

Question 52

Regulatory proteins can be ________ (modify histones)

Answer 52

Chromatin modifying

Question 53

Regulatory proteins can be ___________ (move nucleosomes)

Answer 53

ATP-dependent chromatin remodeling

Question 54

_________ promoters tend to be accessible (no nucleosome)

Answer 54

TATA box

Question 55

_________ promoters tend to be bound by nucleosomes and require remodeling factors to remove them

Answer 55

TATA minus

Question 56

The rate-limiting step in transcription from paused promoters is __________

Answer 56

Elongation

Question 57

_________ of metazoan genes pause after 20-60nts

Answer 57

~70%

Question 58

_______ is a negative elongation factor

Answer 58

NELF

Question 59

Pause release is mediated by ______ – Ser 2 Phosphorylation

Answer 59

P-TEFb (positive transcription elongation factor)

Question 60

_______ is converted into a positive elongation factor via Phosphorylation

Answer 60

DSIF

Question 61

_________ can be part of the super-elongation complex (SEC)

Answer 61

P-TEFb

Question 62

Sequence-specific TFs can modulate RNA polII _______, _________, or ______!

Answer 62

initiation, elongation, or both

Question 63

To identify the promoter of a specific gene, one could generate _______ data for RNA-polymerase and look for peaks at the 5’ end of the gene

Answer 63

ChIP

Question 64

To identify the promoter of a specific gene, one could use _________ to identify the 5’ end of the gene using available RNA-seq analysis and then search for signature motifs found in promoters (TATA, lnr, DPE, etc).

Answer 64

bioinformatics

Question 65

To test if a region has promoter activity, one could use ________ assays to assess for promoter activity in cells.

Answer 65

reporter

Question 66

To determine if a specific DNA sequence is required for promoter activity, one could ________ the sites and test again in reporter assays to assess for promoter activity in cells.

Answer 66

mutate