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molgen > Chapter 18 - Eukaryotic Transcription > Flashcards

Chapter 18 - Eukaryotic Transcription Flashcards

1
Q

Differences from prokaryotic transcription

A

Chromatin must be relaxed before RNA polymerase can access the promoter
Requires many external initiation factors
General transcription factors
Multiple promoters and control elements
Multiple RNA polymerases responsible for transcription of different classes of genes

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2
Q

RNA Polymerase I Promotors

A

Transcribes rRNA genes from a single promoter type
Exists as a holoenzyme that is recruited to the promoter as a large complex by transcription factors
Core promoter is sufficient for initiation of transcription

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3
Q

core promoter

A

Surrounds the start point
Primarily GC rich
Efficiency is increased by interactions with upstream promoter (control) element

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4
Q

UBF

A

Required for high initiation frequency
Twists DNA to bring UPE and core promoter in close proximity to one another
Maintains open chromatin structure
Prevents H1 binding

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5
Q

SL1

A

Responsible for RNAP I recruitment
Binds to core promoter
Contains a TATA-binding protein

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6
Q

Three types of RNAP III promoters

A

Type 1
5S rRNA genes
Internal promoters located downstream of start
Type 1 and 2
tRNA genes
Internal promoters located downstream of start
Type 3
snRNA genes
Located upstream of start
Contains TATA box
Similar to RNAP II promoter

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7
Q

TFIIIB

A

Binds at start site
Its sole presence is sufficient for RNAP III to identify and bind start site

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8
Q

All RNAP III promoters require … to assist the binding of TFIIIB at the correct location

A

TFIIIC assembly factors

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9
Q

RNA polymerase II requires

A

general transcription factors to initiate transcription

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10
Q

RNAP II promoters are more diverse in their

A

structure than the bacterial promoter or the other eukaryotic RNAP promoters

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11
Q

TATA box

A

Common component of RNAP II promoters
The most important element for many RNAP II promoters
Similar in sequence to -10 consensus in bacteria
Often surrounded by GC rich sequences
BRE sequence
Located at approximately -30
Is the only upstream promoter element found at a relatively fixed position

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12
Q

initiator element

A

INR
covers transcription start site

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13
Q

downstream promoter element

A

DPE
common component of those RNAP II promoters that do not contain a TATA box

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14
Q

Each class of eukaryotic RNAP is assisted by a

A

positioning factor that contains TBP and other components

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15
Q

TATA-binding protein was originally identified as a

A

protein that binds to the TATA box in RNAP II promoters

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16
Q

TFIID

A

Positioning factor required by RNAP II
Also contains 14 subunits called TAFs
TBP associated factors
Multiple TFIID variants contain different combinations of TAFs
Different TFIID variants are tissue-specific

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17
Q

TBP

A

The positioning factor recognizes the promoter in different ways for different RNAPs

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18
Q

RNAP III
TFIIIB binds next to

A

TFIIIC

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19
Q

RNAP I
SL1 binds in conjunction with

A

UBF

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20
Q

RNAP II
TFIID is

A

solely responsible for binding

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21
Q

TBP binds to the

A

minor groove in DNA

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22
Q

nucleosome also bind in the

A

minor groove

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23
Q

upon binding, TBP bends the DNA

A

80 degrees

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24
Q

Three basic types of chromatin with respect to transcriptional activity

A
  1. Inactive gene with closed chromatin
  2. Potentially active gene with open chromatin and a bound RNAP
    Poised gene
    Basal apparatus is assembled but cannot transcribe without additional signal
  3. Gene undergoing initiation in open chromatin
    Active transcription begins
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25
Q

Transcription initiation complex steps

A
  1. TBP subunit of TFIID directs transcription factor to TATA box
  2. TFIIB binds
  3. TFIIF binds
  4. RNAP II is recruited to the promoter
  5. TFIIH binds
  6. TFIIE binds
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26
Q

TFIIB

A

Is recruited to the promoter along with RNAP II

27
Q

TFIIF

A

Is recruited to the promoter along with RNAP II
Large subunit contains DNA helicase activity
Small subunit has some homology to bacterial sigma factor regions that bind core polymerase

28
Q

RNAP II is recruited to the promoter

A

TFIIB binds near RNA exit site and may influence switch from abortive initiation to promoter escape
TFIIB also inserts into the active site of RNAP II and assists TFIID with stabilization of promoter melting

29
Q

TFIIH

A

10 subunits, almost as large as RNAP II
Kinase that phosphorylates the CTD of RNAP II
Interacts with RNAP II downstream of start site
Involved in promoter escape
Involved in nucleotide excision repair pathways

30
Q

TFIIE

A

Extends region covered by the apparatus to +30 degrees

31
Q

TFIID binds to the INR via interactions with

A

TAFs

32
Q

Some TATA-less promoters lack

A

unique transcription start sites

33
Q

After the transcription initiation complex forms, TFIIH

A

hydrolyzes ATP to denature DNA at the transcription start site

34
Q

RNAP II begins to make short unstable transcripts 4-5 nt in length

A

Similar to the abortive initiation events seen in bacterial initiation
Short transcripts are not base paired correctly
Promoter proofreading?

35
Q

RNAP II must undergo conformational changes for

A

promoter clearance

36
Q

promoter clearance

A

Ability of RNAP to release promoter and elongate transcript
Controlled by CTD and enhancers
Key determining factor of whether a gene is actually transcribed

37
Q

Phosphorylation of CTD tail of RNAP II is required for

A

promoter and transcription factor release

38
Q

Phosphorylation is facilitated by a kinase complex that includes TFIIH and Cdk9

A

TFIIH and Cdk9

39
Q

TFIIH and Cdk9

A

TFIIH phosphorylates serines in the fifth position of each repeat
Cdk9 is also involved in cell cycle control

40
Q

CTD is also involved in mRNA processing

A

Phosphorylated CTD serves as a recognition site for capping, tailing, and splicing enzymes

41
Q

RNAP II changes conformation

A

Disengages from general transcription factors
Tightens interactions with DNA
Acquires new proteins that increase RNAP II processivity

42
Q

Transcriptional regulators bind to enhancer regions to influence the assembly of the

A

general transcription factors and RNAP II to the gene control region

43
Q

Enhancers are

A

cis-regulatory sequences located a variable distance from core promoter

44
Q

Regulators that bind enhancers can be classified by their potential effect on transcription

A

activators and repressors

45
Q

Other regulators called … also interact with activators and repressors
But do not usually directly bind DNA

A

coactivators and co-repressors

46
Q

true activators

A

that bind specific DNA elements and the basal machinery at the promoter

47
Q

chromatin remodeling activators

A

recruit chromatin modification enzymes and remodeling complexes

48
Q

architectural modifying activators

A

bend DNA in order to bring factors bound apart on linear duplex into close proximity

49
Q

mediator

A

A large protein complex that allows the transcriptional regulators, general transcription factors, and RNAP II to assemble at the promoter
Correctly positions TFIIH near the tail of RNAP II, which facilitates CTD phosphorylation

50
Q

These new regulators act in three ways to facilitate elongation

A
  1. Recruit chromatin remodeling complexes to release chromatin that is blocking RNAP II movement
  2. Interacts with RNAP II via a coactivator to unpause enzyme
  3. Act as or recruit elongation factors
51
Q

Elongation factors decrease the likelihood that RNAP will

A

dissociate from the DNA during elongation

52
Q

Major function of elongation factors

A

is to help RNAP move through nucleosomes

53
Q

Chromatin must be partially remodeled to facilitate transcription

A

Nucleosome sliding
Nucleosome removal
Replacement with histone variant nucleosomes
Histone modifications

54
Q

Histone modification is an important part of

A

both transcription initiation and elongation

55
Q

Initiation can be facilitated by

A

activators that recruit coactivators that contain histone modifying and chromatin remodeling enzymes

56
Q

During elongation, nucleosomes ahead of RNAP are

A

acetylated, removed, and deposited behind the polymerase

57
Q

Deposited nucleosomes are rapidly

A

deacetylated and methylated by polymerase-associated enzymes

58
Q

FACT

A

FAcilitates Chromatin Transcription
Heterodimeric protein factor
Acts like a transcription elongation factor
Not part of RNA polymerase
Only associates during elongation
Helps facilitate H2A-H2B dimer release from octamers

59
Q

FACT steps

A

FACT releases one H2A-H2B dimer from each octamer as RNA polymerase approaches
Remaining “hexosome” remains on DNA as RNA polymerase passes
After RNA polymerase passes, FACT adds H2A-H2B dimer back to “hexosome” to reform octamer
Chromatin structure is maintained

60
Q

No FACT present

A

RNA polymerase and elongation factors peel some DNA from nucleosomes
Aided by supercoiling
DNA binding region of nucleosome is now accessible
Upstream DNA is looped and binds to exposed nucleosome
Nucleosome is captured by upstream DNA and transferred upstream and behind RNA polymerase

61
Q

Eukaryotic transcription is thought to be … by default because of chromatin structure

A

off

62
Q

Eukaryotic repressors are able to

A

both actively turn “off” a gene that has been activated and to further repress a gene that is already “off”

63
Q

Eukaryotic repressors action

A

Prevent activator binding and action
Recruit histone modification and chromatin remodeling enzymes

molgen (28 decks)

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