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MolCell Mega Class > GEBELEIN 2 > Flashcards

GEBELEIN 2 Flashcards

1
Q

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

A

super-elongation complex (SEC)

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2
Q

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

A

P-TEFb

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3
Q

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

A

PIC

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4
Q

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

A

kinases

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5
Q

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

A

Core promoters

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6
Q

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

A

promoter-proximal elements, enhancers

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7
Q

These control elements function by recruiting ___________.

A

sequence-specific TFs

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8
Q

________% of the genome is regulatory sequence.

A

20

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9
Q

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

A

10x

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10
Q

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

A

non-coding DNA

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11
Q

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

A

enhancer

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12
Q

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

A

Sonic-hedgehog (Shh)

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13
Q

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

A

Modularity

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14
Q

Enhancers can be located _______ of the promoter.

A

up or downstream

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15
Q

Enhancers can be located in ________ regions.

A

intronic

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16
Q

Enhancers can be located varying distances up to _______ away.

A

1mb

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17
Q

Enhancers regulate the _________ of transcription.

A

rate

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18
Q

Enhancers regulate the _______ of transcription.

A

quantity

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19
Q

Enhancers regulate the _______ of transcription.

A

time

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20
Q

Enhancers regulate the _______ of transcription.

A

place

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21
Q

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

A

TFs

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22
Q

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

A

conserved

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23
Q

Different enhancers for different tissues is an example of ________.

A

Modularity

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24
Q

Separate enhancers and ________ contribute to making stripes in flies.

A

combinatorial control

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25
Q

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

A

even-skipped (eve)

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26
Q

________ encode ‘instructions’ for gene expression.

A

Cis-regulatory modules (CRMs)

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27
Q

A ‘typical’ CRM is _______ bps.

A

~200

28
Q

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

A

~3-10

29
Q

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

A

activation, repression, or both

30
Q

The ________ binds DNA in a sequence-specific manner.

A

DNA binding domain

31
Q

Examples of DNA binding domains include _________.

A

homeodomain, zinc finger

32
Q

Regulatory domains activate or repress by recruiting _________.

A

co-regulatory proteins

33
Q

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

A

Histone acetyltransferases (HATs), histone deacetylases (HDACs)

34
Q

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

A

binding site preferences

35
Q

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

A

Critical binding sequences

36
Q

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

A

RNA polII

37
Q

_______ is targeted to the HRE DNA sequence

A

GR

38
Q

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

A

regulatory

39
Q

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

A

SWI/SNF

40
Q

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

A

p300/CBP

41
Q

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

A

ARC/DRIP/TRAP

42
Q

The Mediator interacts with ________ to promote looping.

A

Cohesion Complexes

43
Q

The Mediator links distant _______ to _________.

A

enhancers, promoters

44
Q

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

A

PIC

45
Q

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

A

SEC

46
Q

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

A

preinitiation complex (PIC)

47
Q

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

A

PolII release

48
Q

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

A

SEC/cdk9/P-TEFb kinase

49
Q

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

A

Hairy

50
Q

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

A

GTFs/RNA polII

51
Q

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

A

enzyme activities

52
Q

Regulatory proteins can be ________ (modify histones)

A

Chromatin modifying

53
Q

Regulatory proteins can be ___________ (move nucleosomes)

A

ATP-dependent chromatin remodeling

54
Q

_________ promoters tend to be accessible (no nucleosome)

A

TATA box

55
Q

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

A

TATA minus

56
Q

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

A

Elongation

57
Q

_________ of metazoan genes pause after 20-60nts

A

~70%

58
Q

_______ is a negative elongation factor

A

NELF

59
Q

Pause release is mediated by ______ – Ser 2 Phosphorylation

A

P-TEFb (positive transcription elongation factor)

60
Q

_______ is converted into a positive elongation factor via Phosphorylation

A

DSIF

61
Q

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

A

P-TEFb

62
Q

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

A

initiation, elongation, or both

63
Q

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

A

ChIP

64
Q

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).

A

bioinformatics

65
Q

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

A

reporter

66
Q

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.

A

mutate

MolCell Mega Class (21 decks)

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