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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
Transcription initiation complex steps
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
26
TFIIB
Is recruited to the promoter along with RNAP II
27
TFIIF
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
RNAP II is recruited to the promoter
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
TFIIH
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
TFIIE
Extends region covered by the apparatus to +30 degrees
31
TFIID binds to the INR via interactions with
TAFs
32
Some TATA-less promoters lack
unique transcription start sites
33
After the transcription initiation complex forms, TFIIH
hydrolyzes ATP to denature DNA at the transcription start site
34
RNAP II begins to make short unstable transcripts 4-5 nt in length
Similar to the abortive initiation events seen in bacterial initiation Short transcripts are not base paired correctly Promoter proofreading?
35
RNAP II must undergo conformational changes for
promoter clearance
36
promoter clearance
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
Phosphorylation of CTD tail of RNAP II is required for
promoter and transcription factor release
38
Phosphorylation is facilitated by a kinase complex that includes TFIIH and Cdk9
TFIIH and Cdk9
39
TFIIH and Cdk9
TFIIH phosphorylates serines in the fifth position of each repeat Cdk9 is also involved in cell cycle control
40
CTD is also involved in mRNA processing
Phosphorylated CTD serves as a recognition site for capping, tailing, and splicing enzymes
41
RNAP II changes conformation
Disengages from general transcription factors Tightens interactions with DNA Acquires new proteins that increase RNAP II processivity
42
Transcriptional regulators bind to enhancer regions to influence the assembly of the
general transcription factors and RNAP II to the gene control region
43
Enhancers are
cis-regulatory sequences located a variable distance from core promoter
44
Regulators that bind enhancers can be classified by their potential effect on transcription
activators and repressors
45
Other regulators called ... also interact with activators and repressors But do not usually directly bind DNA
coactivators and co-repressors
46
true activators
that bind specific DNA elements and the basal machinery at the promoter
47
chromatin remodeling activators
recruit chromatin modification enzymes and remodeling complexes
48
architectural modifying activators
bend DNA in order to bring factors bound apart on linear duplex into close proximity
49
mediator
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
These new regulators act in three ways to facilitate elongation
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
Elongation factors decrease the likelihood that RNAP will
dissociate from the DNA during elongation
52
Major function of elongation factors
is to help RNAP move through nucleosomes
53
Chromatin must be partially remodeled to facilitate transcription
Nucleosome sliding Nucleosome removal Replacement with histone variant nucleosomes Histone modifications
54
Histone modification is an important part of
both transcription initiation and elongation
55
Initiation can be facilitated by
activators that recruit coactivators that contain histone modifying and chromatin remodeling enzymes
56
During elongation, nucleosomes ahead of RNAP are
acetylated, removed, and deposited behind the polymerase
57
Deposited nucleosomes are rapidly
deacetylated and methylated by polymerase-associated enzymes
58
FACT
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
FACT steps
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
No FACT present
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
Eukaryotic transcription is thought to be ... by default because of chromatin structure
off
62
Eukaryotic repressors are able to
both actively turn “off” a gene that has been activated and to further repress a gene that is already “off"
63
Eukaryotic repressors action
Prevent activator binding and action Recruit histone modification and chromatin remodeling enzymes

MOLGEN (28 decks)

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