1
Q
What do general transcription factors do?
A
- Help position RNA polymerase at eukaryotic promoters
2
Q
TFIID role in transcription initiation
A
- Recognizes TATA box and other DNA sequences near the transcription start point
- Finds the right location & recruits RNA polymerase
3
Q
TFIIH
A
- Unwinds DNA at transcription start point, phosphorylates Ser5 of the RNA polymerase C-terminal domain (CTD), releases RNA polymerase from promoter
- Phosphorylates tail & RNA polymerase can leave promoter and transcribe
4
Q
RNA Polymerase II
A
- Transcribes protein coding genes
- Requires 5 general transcription factors (TFIID, TFIIB, TFIIF, TFIIE, TFIIH) for eukaryotes
5
Q
What is chromatin?
A
- Eukaryotic DNA packaged to allow certain areas to be transcribed
- Allows a lot of DNA to package into a small space
6
Q
What is the role of the mediator?
A
- An intermediate between regulatory proteins proteins & RNA polymerase, provides a large surface for them to interact
7
Q
Coactivator
A
- Binds to DNA regulatory proteins & turn on gene expression
- Don’t directly bind to DNA
8
Q
Corepressors
A
- Binds to DNA regulatory proteins & turn off gene expression
9
Q
Eukaryotic activator proteins
A
- DNA binding domain to a cis element (DBD): recognizes specific DNA sequence (bottom part)
- Activation domain (AD): accelerates frequency/rate of transcription (top part)
- Can turn on expression as long as its at the right place/right time
10
Q
What does the recognition sequence require to bind to DBD?
A
- Must be the recognition sequence to match the DNA binding protein (bottom half), not the activation domain
11
Q
How do activator proteins activate transcription?
A
- Attract, position, modify: general transcription factors, mediator, RNA polymerase II
- Either: directly by acting on these components (bringing them to promoter) OR indirectly by modifying chromatin structure (so transcriptional machinery can assemble)
12
Q
Activator protein direct binding
A
- Bind to transcriptional machinery or the mediator & attract them to promoters (prokaryotic activators)
13
Q
4 ways activator protein alters chromatin structure
A
- Nucleosome sliding
- Remove nucleosomes
- Replace histones (histone chaperones)
- Covalently modify histones (on specific histone tails by ‘writers’ & code reader provides meaning)
14
Q
Histone modifications
A
- Add phosphate group: phosphorylation (enzyme = kinase)
- Add acetyl group: acetylation (enzyme = acetyltransferase)
- Add methyl group: methylation (enzyme = methyltransferase)
15
Q
Human interferon gene regulation as a histone code example
A
- Activator protein binds to chromatin DNA & attracts a histone acetyltransferase (HAT)
- HAT acetylates lysine 9 of histone H3 & lysine 8 of histone H4
- Activator protein attracts a histone kinase (HK)
- HK phosphorylates serine 10 of histone H3 ONLY after acetylation of lysine 9
- Serine modification signals acetyltransferase to acetylate lysine 14 of histone H3 (histone code for transcription initiation is written)
- TFIID & a chromatin remodeling complex bind to modified histone tails and initiate transcription (code readers)
16
Q
Eukaryotic mechanisms to inhibit transcription
A
- Competitive DNA binding
- Masking the activation surface
- Direct interaction with the general transcription factors
- Recruitment of chromatin remodeling complexes
- Recruitment of histone deacetylases
- Recruitment of histone methyl transferase
17
Q
Competitive DNA binding
A
- Activator & repressor compete for DNA binding
18
Q
Masking the activation surface
A
- Can’t activate transcription because repressor connects to activator
19
Q
Direct interaction with general transcription factors
A
- Repressor interferes with TFIID’s ability to initiate transcription
20
Q
Recruitment of chromatin remodeling complexes
A
- Close up chromatin to stop transcription (histone sliding, replacement)
21
Q
Recruitment of histone deacetylases
A
- Removes acetyl groups (represses gene expression)
22
Q
Recruitment of histone methyl transferase
A
- Methylates histones, creates repressive form of chromatin that can be inherited
23
Q
Histone reader & writer complexes
A
- Establish a repressive form of chromatin
- Histone modifying enzyme (methyl transferase) placed onto histone by writer
- Reader recognizes DNA methylase enzyme and methylates nearby cytosines in DNA
24
Q
What do DNA methyl-binding proteins do?
A
- Bind methyl groups & stabilize structure of chromatin
25
Epigenetic inheritance
- Methylation & gene expression patterns can be inherited
- Inheritance of some phenotype that doesn't require modifications to DNA sequence
BIO230 Part 1
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