1
Q
What are the two major differences between DNA replication and RNA transcription?
A
- DNA replication copies the entire genome once and only once per cell cycle; RNA transcription selectively copies only certain parts of the genome from one to multiple times.
- Both DNA strands serve as templates for DNA replication; only one of the DNA strands serves as a template on which the RNA strand is built in RNA transcription.
2
Q
In RNA transcription, which strand is used as the template?
A
The non-coding/antisense strand
3
Q
RNA transcripts dissociate from the DNA template a few ribonucleotides behind the point of synthesis. What two things does this allow for?
A
- Multiple transcription of the same gene to occur at the same time.
- Translation to occur rapidly
4
Q
True or false: RNA polymerase requires primers
A
False; it catalyzes RNA synthesis in the absence of primers (i.e. different that the DNA polymerase)
5
Q
What does RNA transcription lack that is present in DNA replication?
A
Extensive proofreading mechanisms
- Still has proofreading ability, but less
6
Q
Eukaryotes have __ RNA polymerase(s), prokaryotes have __ RNA polymerase(s).
A
Eukaryotes have 3 polymerases, prokaryotes have 1 polymerase.
7
Q
RNA polymerase in all organisms contains how many subunits?
A
2 alpha and 2 beta subunits
8
Q
Eukaryotic pol I, II, and III have ____ subunits, which are…
A
Eukaryotic pol I, II, and III have 7-11 extra subunits, which are mainly specific to each polymerase
9
Q
What does RNA pol I transcribe in eukaryotes?
A
Large RNA (rRNA precursor)
10
Q
What does RNA pol II transcribe in eukaryotes?
A
Protein-encoding genes
11
Q
What does RNA pol III transcribe in eukaryotes?
A
tRNA and 5S rRNA transcription
12
Q
What are the 3 phases of transcription?
A
Initiation, elongation and termination
13
Q
What DNA element determines which DNA stretch undergoes transcription?
A
The promoter
14
Q
What are the 3 steps of transcription initiation?
A
- Formation of a closed complex by binding a Pol to the promoter (formation of the pre-initiation complex, transcription bubble still not formed)
- Closed complex transformed into an open complex (i.e. transcription bubble, created by the melting of the double helices)
- Initial transcribing complex makes the first 10 ribonucleotides
15
Q
Describe transcription elongation and termination
A
- Continual RNA synthesis
- Unwinds the DNA in the front and re-anneals it behind
- Emergence of the growing RNA from the template
- Proofreads
Termination: transcription stops and the RNA product is released
16
Q
Prokaryotes require _ initiation factor(s), eukaryotes require _ initiation factors
A
Prokaryotes require 1 initiation factor (Sigma), eukaryotes require several initiation factors (i.e. general transcription factors) for promoter-specific initiation
17
Q
What 4 DNA elements are present at the core promoter?
A
- BRE: TFIIB recognition element
- Inr: Initiator
- TATA box
- DPE: Downstream promoter element
18
Q
What proteins recognize the core promoter elements? And which elements do each of them recognize?
A
- TFIIB recognizes BRE
- TBP recognizes the TATA box
- TFIID recognizes the Inr and the DPE
19
Q
How is the core promoter defined?
A
The minimal sequence needed for accurate transcription initiation in vitro
20
Q
What is contained upstream of the core promoter?
A
Regulatory sequences required for efficient transcription in vivo
21
Q
What are 6 examples of sequence elements contained upstream of the core promoter?
A
- Promoter proximal elements
- Upstream activator sequences (UASs)
- Enhancers
- Silencers
- Boundary elements
- Insulators
22
Q
How do you determine the sequence of TF addition to the promoter in vitro?
A
By adding one TF at a time
23
Q
The TBP (TATA-binding protein) is associated with…
A
~10 other TAFs (TBP-Associated Factors)
24
Q
What is the order of the general transcription factor binding/steps to initiate transcription? (6 steps)
A
- TBP to TATA box
- TFIID to TATA box
- TFIIA and TFIIB bind
- Pol II with TFIIF binds
- TFIIE and TFIIH bind which completes the pre-initiation complex
- CTD becomes phosphorylated, promoter escape occurs and transcription elongation begins
25
TFIIB binding and function
- Binds the pre-initiation complex after TBP is bound
- May function in bridging between TATA-bound TBP and Pol II
26
TFIIF binding and function
Recruited to promoter with pol II
- Pol II-TFIIF stabilizes the DNA-TBP-TFIIB complex and recruits TFIIE and TFIIH
27
TFIIE function
Recruits and regulates TFIIH
28
Largest and most complex TAF (TBP-associated factors)
TFIIH
29
TFIIH function
- Controls ATP-dependent transition of the pre-initiation complex to the open complex
- Phosphorylates Pol II CTD (C-terminal domain) and causes promoter melting and escape
- Also functions in nucleotide excision repair
30
Define the pre-initiation complex
Protein complex containing Pol and general transcription factors.
31
Describe the recruitment of the TFIID complex, and what proteins make up the TFIID complex
TFIID recognizes the TATA element
- TFIID + TBP + 11 TAFs (TBP Associated factors)
- TBP (TATA- Binding protein) binds TATA box
32
How does TBP bind to the TATA box?
- TBP binds the minor groove of the TATA element through its β sheet (in general, it's the α helix: major groove binding)
- TBP inducing induces the minor groove to undergo conformational change (widens the minor groove to almost flat and bends the DNA). This changes the topology a bit of the DNA -> opens the structure slightly
33
What binds to the promoter after TFIID binds? (2)
TFIIA and TFIIB
34
What is determined by the TFIIB-TBP complex?
Transcription direction
- It defines asymmetric assembly of the pre-initiation complex and unidirectional transcription
35
True or false: TFIIB binds the minor groove like TBP
True
36
Describe the structure of the CTD (carboxy-terminal domain) of Pol II of RNA polymerase II, and the reasoning for this structure
CTD of Pol II has repeats of Ser and Tyr for phosphorylation
37
What binds to the promoter after TFIIA and TFIIB bind? What is the structure of the DNA up to this point?
Pol II with TFIIF binds
- DNA is still in closed form up to this point
38
True or false: Pols I and III also have repeats for phosphorylation
False
39
What transcription factors bind the the pre-initiation complex after TFIIF?
TFIIE and TFIIH bind to complete the pre-initiation complex
40
TFIIH function after binding
Induces promoter melting with ATP hydrolysis and phosphorylates Pol II CTD, resulting in promoter escape
41
What occurs after TFIIE and TFIIH bind to the pre-initiation complex?
CTD becomes phosphorylated, promoter escape occurs, and transcription elongation begins
- The initiation stage is complete
42
What does transcription initiation require in vivo? Why?
Additional proteins are required because the DNA template in vivo is in chromatin form
43
What 4 additional proteins are required for in vivo transcription initiation?
1. Activator proteins that recruit Pol and stabilizes Pol: promoter interaction; also binds to chromatin remodeler complexes
2. Chromatin remodelers that modify nucleosome structure to facilitate transcription
3. HAT: is part of the chromosome remodelling complex
4. Mediator complex that bridges the CTD of the Pol and the activator; also regulates TFIIH
44
True or false: histone-modifying enzymes are often required for in vivo transcription initiation
True
45
Describe yeast and human mediators (3)
- Organized in modules (i.e. sub-complexes) reflecting the different methods of isolation
- Have similar shape and are larger than RNA pols
- The function of most individual subunits is unknown
46
True or false: many of the mediator subunits are conserved between yeast and humans
True
47
Which mediator subunit is required for Pol II transcription in vivo?
Med17
48
Describe a technique used to study or identify components of the mediator complex
Immunoprecipitation followed by SDS-PAGE
To isolate protein X:
- First design anti-X antibody against "X" protein
- After immunoprecipitation, the isolated proteins are separated by SDS-PAGE, a technique that resolves proteins by size
- SDS-PAGE ca help identify proteins that interact with the protein of interest. By analyzing the gel, researchers can infer which proteins are part of the same complex.
49
____ facilitates elongation through nucleosomes
FACT
- protein that stands for FAcilitates Chromatin Transcription
50
What proteins make up the FACT dimer?
1. Spt16:H2A:H2B
2. SSRP1:H3:H4
51
FACT facilitates transcription elongation through...
Nucleosomes
52
Describe how FACT dimer facilitates elongation through nucleosomes
1.Spt16 disassembles H2A:H2B from the nucleosome during transcription
2. Spt16 aids in restoring H2A:H2B once the transcription bubble passes a given nucleosome
53
What happens to most initiation factors (e.g. TFIIB, TBP, etc) during transcription elongation?
Most initiation factors dissociate from Pol II once Pol II is activated
54
____ ______ are recruited to the CTD tail of Pol II during transcription
Elongation factors
55
What does the recruitment of elongation factors depend on?
The phosphorylation state of the CTD tail
56
Define elongation factors
Factors that stimulate elongation
57
ELL protein family and TFIIS elongation factors (increase/decrease) the rate of elongation by...
ELL protein family and TFIIS elongation factors increase the rate of elongation by limiting the time that Pol pauses
- TFIIS can also proofread the new transcript
58
What are 3 categories of RNA processing enzymes?
1. 5' capping enzymes
2. Splicing factors
3. 3' polyadenylation and cleavage factors
59
What do cleavage factors do during RNA processing?
Cleave theRNA from the polymerase
- Frees up the RNA, post-transcriptional modifications then occur
60
Why is research on RNA so limited?
Because RNA is so unstable
- 5' capping and 3'polyA tail helps with working with RNA
61
In what order are the following post-transcriptional modification enzymes recruited to the RNA transcript?
- Components of splicing machinery
-PolyA tail and cleavage factors
- Capping enzyme
1. Capping enzyme
2. Components of splicing machinery
3. Polyadenylation and cleavage factors
62
True or false: splicing may occur before the completion of RNA synthesis
True
- Splicing factors may be recruited once introns are exposed
63
The RNA processing factors recruited depends on...
The phosphorylation state of the CTD tail
64
What are the three steps of 5'RNA cap formation?
1. RNA triphosphatase removes the γ-phosphate at the 5' end of the transcript
2. guanyltransferase adds the GMP moiety to the terminal β-phosphate
3. Methyltransferase adds a 7 methyl group to the guanine base
65
The 5' cap on RNA is specifically...
7-methylguanylate
66
What are the 2 functions of the 5' cap?
1. Stabilizes the transcript
2. Signals that the transcript is correctly processed
67
What are the seven steps of 3' polyadenylation?
1. RNA Pol II encounters and transcribes the poly-A signal (usually AAUAAA)
2. Phosphorylated CTD tail recruits polyadenylation enzymes CPSF
3. RNA Pol II continues transcribing, but falls off shortly
4. CPSF + CstF + other proteins cleave downstream of the poly-A signal
5. CstF leaves
6. poly-A polymerase (PAP) adds ~200 adenines (A) to the 3' end of the poly-A signal RNA
7. poly-A binding protein (PBP) coats the As
68
CstF
Cleavage stimulatory factor
69
CPSF
Cleavage polyadenylation specific factor
70
What are the two functions of the Poly A tail?
1. Stabilizes the mRNA
2. Signals correct 3' end processing
71
What are the two main models of transcription termination in vivo?
1. Torpedo Model of Termination
2. Allosteric Model of Termination
72
Describe the Torpedo Model of Termination
1. 5' to 3' exonuclease (torpedo) is associated with RNA pol. Torpedo = Rat1/hXrn2
2. Once the polyA signal is exposed on the RNA transcript, the RNA transcript is cleaved from the RNA pol
3. The torpedo exonuclease then degrades the second RNA as it has an uncapped end
4. Degradation of the second RNA destabilizes Pol II, causing it to dissociate from the DNA template and terminate transcription.
73
The allosteric model of termination is a ______-dependent model
Processivity
74
Describe the allosteric model of termination
1. RNA pol is highly processive when first transcribing the DNA
2. Once the RNA pol transcribes the poly-A signal, the Pol II undergoes a conformational change.
3. The conformational change of the Pol II decreases the processivity of the Pol, which reduces the affinity of the Pol for the DNA
4. Eventually, the RNA pol dissociates
75
There are (high/low) levels of Pol I transcription in cells
High
76
Pol I is dedicated to transcribing an rRNA precursor in cells (which comes from one gene). Why do we need something with such high transcriptional activity dedicated to just one gene?
This rRNA gene has many isoforms (RNA transcripts from the same gene which have had different exons removed), so high transcriptional activity is required
77
Describe what proteins are recruited before Pol I is recruited to transcribe the rRNA gene (3 steps)
1. UBF binds first to the UCE (upstream control element)
2. SL1 = TBP + 3 TAFs bind to the core promoter after
3. Recruitment of RNA pol I
78
What is unique about the promoters for tRNA and 5S RNA genes that are transcribed from pol III?
- The promoters are internal to the tRNAs or 5S RNAs
- Transcription starts upstream of the promoter
79
Describe what proteins bind to the tRNA/5S rRNA promoter before Pol III is recruited (3 steps)
1. TFIIIC binds both box A and B
2. TFIIIB and TBP are recruited upstream of TFIIIC after TFIIIC binds
3. Pol III is then recruited, and binsd the start site which is located between TFIIIB/TBP and TFIIIC
80
What is the primary point of gene regulation?
Transcription initiation
81
In general, transcription is controlled by...
Activators and repressors
82
What does upstream of the core promoter contain?
The regulatory sequences required for efficient transcription in vivo
83
Define promoter
Region of DNA involved in pre-initiation complex binding
84
Define regulatory binding sites
Binding sites for different transcription factors
85
Define regulatory sequences
The entire collection of regulator binding sites for a given gene
86
Define enhancer
A tight cluster of regulatory binding sites that can affect long distances at either upstream or downstream of a gene
87
Define the UAS (Upstream Activating Sequence)
An "enhancer" in yeast, only found upstream of a gene and usually not a great distance
88
Define an insulator
Blocks promoter activation by binding activators at the enhancer
89
There is (increasing/decreasing) complexity of regulatory sequences from a bacterial gene to human
Increasing
90
Transcription factors typically contain what 2 domains?
Distinct DNA-binding and activation domains
91
Transcription activators often act as a _____, and sometimes recognize _____
Transcription activators often act as a dimer, and sometimes recognize palindromic sequences
92
(The same/different) activators bind to each regulatory sequence in a regulatory site; all regulatory sites (are/are not) necessarily bound at the same time
Different activators bind to each regulatory sequence in a genome; all regulatory sites are not necessarily bound at the same time
93
What was an example of a transcription activator that we discussed in lecture and what gene does it bind?
Gal4, which activates the Gal1 gene in yeast
94
Describe the UAS near the promoter of the Gal1 gene in yeast
- Explain how this differs from human promoters
Has 4 regulatory sequences, where each sequence will bind a dimer of Gal4
- Human promoters are even more complex
95
What is required on the transcription activator (factor), apart from the DNA-binding domain, for eukaryotic transcription initiation?
An activation domain is required for eukaryotic transcription initiation
96
True or false: The activating domain of a transcription factor can activate another transcription factor by binding to its DNA-binding domain (through formation of a chimera/hybrid/recombinant)
True
97
What is a yeast two-hybrid assay in general and what is it widely used for?
- A protein-protein binding assay based on properties of yeast TFs
- Widely used to search for binding proteins through a genetic screen
- Helps us understand protein-protein interactions
98
In a yeast two-hybrid assay, what transcriptional result is observed when protein B ("prey" protein) is tethered to an activating domain, but the DNA-binding domain is absent?
No transcription of reporter gene
99
In a yeast two-hybrid assay, what transcriptional result is observed when protein A ("bait" protein) is tethered to a DNA-binding domain but protein B with activating region is absent?
No transcription of reporter gene
100
In a yeast two-hybrid assay, what transcriptional result is observed when protein B ("prey" protein) is tethered to an activating domain, and bound the protein A ("bait" protein)?
Transcription of the reporter gene
101
How can His be used in a yeast two-hybrid assay
Put yeast in His- environment, cells will die if they don't express His as a reporter gene -> can use to see which proteins interact to activate transcription
102
Describe the "anatomy" of a DNA- binding domain (4)
1. Helix-turn-helix motif
- homeodomain proteins
2. Zinc-containing DNA-binding domains
- Zinc finger (e.g. TFIIIA)
- Zinc cluster (e.g. Gal4)
3. Leucine-zipper motif (e.g. yeast GCN4)
4. Helix-loop-helix
103
Describe the "anatomy" of activation domains (3)
1. Lack of defined motifs
2. Grouped by amino acid contents
- e.g. Gal4 has an "acidic" activation domain
- e.g. glutamine or proline rich
3. May have "sticky" surfaces, often without single specificity for the protein it binds to
104
Describe how the helices in helix-turn-helix motifs interact with the DNA
- One helix positions the recognition helix by contacting the DNA backbone
- The recognition helix recognizes specific base pairs in the major groove
105
Homeodomain proteins have __ domains
3
106
Homeodomain proteins are found in what organisms?
Found in all eukaryotes
107
The recognition helix in the homeodomain proteins contains which three amino acids?
Ser, Arg and Asn
108
How does a homeodomain contact the DNA?
Helix 3 contacts the major groove, while the tail from helix 1 has some additional contact the minor groove
109
The zinc ion in the zinc-containing domain coordinates with which residues? What does this do?
the zinc ion coordinates with 2 Cys and 2 His residues, stabilizing the protein structural elements
110
Describe the structure of the leucine-zipper motif
- Dimerization of 2 helices that cross over one another
- Lots of leucine near region that binds to the major groove
- Coiled-coil domain contains precisely spaced leucine residues and olds the 2 monomers together
111
Describe the helix-loop helix (HLH) protein and how it binds to the DNA
Dimer of 1 short alpha helix with 1 long alpha helix that bind to the major groove
112
Why is Chromatin Immunoprecipitation (ChIP) used?
Used to determine protein-DNA interactions
113
Describe the steps of ChIP for analysis of TF interactions with DNA (5 steps)
1. Proteins (transcription factors) are cross-linked to DNA fragments by formaldehyde
2. Antibody bound to magnetic beads are added to the solution of DNA fragments. this antibody is specific to the protein of interest bound the the DNA fragment
3. Immunoprecipitate DNA-protein complex using magnet
4. Proteins removed
5. DNA fragment that the protein was bound to is either amplified by PCR or analyzed using a microarray (these procedures both help with sequencig the promoter region that we're interested in)
114
What types of proteins can transcription activators recruit?
1. Recruit other TFs
2. Recruits nucleosome modifiers
3. indirectly recruits RNA pols
4. Recruits factors needed for initiation and elongation
115
How do transcription activators contribute to the complexity and diversity of eukaryotes?
Transcription activators work cooperatively and synergistically to promote combinatorial control, which contributes to the complexity and diversity of eukaryotes
116
What specific proteins do transcription activators recruit to stimulate transcription?
TFIID and mediator directly, and RNA Pol II indirectly
117
True or false: effects of activators are additive and/or synergistic
True
118
The more interactinos with activators, the stronger...
The stimulation of transcription
119
What are 2 ways that activators recruit nucleosome modifiers to improve DNA accessibility for TFs?
1. Activator recruits histone acetylase that modifies histone tails and "opens up" chromatin
2. Activator recruits proteins that use ATP to physically move nucleosomes and expose DNA (SWI/SNF family of modification complexes)
120
Enhancers can act at a...
Great distance, and upstream or down stream of a start site (thousands of bp)
121
Insulators keep enhancers from...
Working at a distance
122
Describe the looped-out model for enhancer function and why enhancers are distance- and orientation-independent
In 3D, the enhancer comes in contact with the pre-initiation complex (through a TF in between) by looping towards the promoter region
- Enhancer can be upstream or downstream to loop around
123
What region regulates expression of a cluster of genes?
The Locus Control Region (LCR)
124
Give an example of a gene cluster regulated by the locus control region (LCR) in humans
5 hemoglobin genes exist in humans that show temporal and spatial regulation in their expression
- Expression order ε -> γ^G -> γ^A -> δ->β
- The appropriate regulators are only found in adult bone marrow (e.g. β globin is expressed in adult bone marrow and have 2 enhancers)
125
How do we switch on the various globin genes in the correct order?
We don't exactly know yet
126
Give an example of genes regulated by LCR in mice
- HoxD genes are involved in patterning the developing limbs
- HoxD gene expression is controlled by GCR (Global Control Region) that works like LCR
- It is not clear exactly how the LCR works, but probably works through chromatin structure
127
Describe the synergistic binding of activators
- The effect of activdators working together is greater than the sum of individual activator alone
- Synergy serves as a checkpoint to ensure proper signals are receive
128
Give two examples of the direct effects of activators that demonstrates synergy
1. Cooperative binding through direct interaction between 2 proteins
2. Both activators interact with a common protein by touching different parts of it
129
Give two examples of the indirect effects of activators that demonstrates synergy
1. First activator recruits a nucleosome remodeler to reveal a binding site a second activator
2. Binding of first activator unwinds the nucleosome, revealing the binding site of a second activator
130
Describe an example of how activators can work synergistically in S. cerevisiae for HO gene expression (signal integration)
SWI5, which is an activator only active in mother cells, can recruit chromatin-remodelling complex and histone acetylase to open SBF DNA binding site up at correct cell cycle stage (G1-S transition), which allows for SBF binding to turn on HO gene transcription
- Both SWI5 and SBF are activators
131
Describe an example of how activators can work synergistically in humans for β-interferon gene
- β-interferon is expressed upon infection
- architectural protein: HMGA1 (High Mobility Group A1) recruits histone modifiers
- HMGA1 binds to the minor groove to help enhancesome assembly by keeping the enhancer straight
132
What are 4 ways that transcription repressors can work?
1. Block RNA pols binding site by occupying the site on the promoter (only found in prokaryotes)
2. Interact with RNA pols at the promoter to inhibit transcription initiation
3. Interfere with the action of activators
4. Recruit histone modifiers to further compact the chromatin structure
133
Describe how repressors can interfere with the action of activators through competition
If there are overlapping DNA binding sites for the activators and the repressors, the repressor can exclude the activator from binding by binding to its repressor binding site
134
Describe how repressors can interfere with the action of activators through inhibition
Repressor binding can result in occlusion of activating region on adjacent TF
135
Describe how repressors can interfere with activators, mediators or RNA pols through direct repression
Can bind directly and inhibit transcription machinery by interfering with activators, mediators or RNA pols
136
Describe how repressors can repress expression through indirect repression
Repressors can recruit histone modifiers, such as deacetylase, that compact chromatin structures
137
A (different/common) regulator can be found in promoters of many genes, to turn on multiple genes at the same time
Common
138
There are (similar/different) combinations of activators/repressors specific to different cells that influence expression
Different
139
What is a common regulator found in all three cells types in S. cerevisiae, being "a" cell, "α" cell and a/α cell (diploid)?
Mcm1
140
What are the gene regulatory proteins in S. cerevisiae "a" cells (haploid), and what is the expression of a-specific genes, α-specific genes and haploid-specific genes?
Gene regulatory proteins: a1 and Mcm1
Target gene expression:
- a-specific genes: Mcm1 binds, transcription on
- α-specific genes: transcription off
- haploid-specific genes: transcription on
141
What are the gene regulatory proteins in S. cerevisiae "α" cells (haploid), and what is the expression of a-specific genes, α-specific genes and haploid-specific genes?
Gene regulatory proteins: α1, α2 (repressor) and Mcm1
Target gene expression:
- a-specific genes: Mcm1 binds with two α2, transcription off
- α-specific genes: α1 binds with Mcm1, transcription on
- haploid-specific genes: transcription on
142
What are the gene regulatory proteins in S. cerevisiae "a/α" cells (diploid), and what is the expression of a-specific genes, α-specific genes and haploid-specific genes?
Gene regulatory proteins: a1, α2 (repressor) and Mcm1
Target gene expression:
- a-specific genes: Mcm1 binds with two α2, transcription off
- α-specific genes: transcription off because α1 is not expressed
- haploid-specific genes: α2 repressor binds with a1, transcription off
143
Why isn't α1 in a/α cell (diploid) expressed?
Because α2 is "dominant", which prevents α1 expression
144
Describe the JAK/STAT pathway (4 steps)
1. Ligand binds the extracellular domain of of JAK kinase receptor (JAK is a tyrosine kinase on the intracellular domain)
2. Phosphorylation of receptor subunits -> causes dimerization
3. STAT's SH2 domain recognizes phospho-Tyr on JAK receptor, results in STAT phosphorylation
4. STAT dimerization and DNA binding (STAT serves as a transcription factor)
145
Describe the mitogen-activated protein kinase (MAPK) pathway (7 steps)
1. Growth factor binds to tyrosine kinase
2. Binding to receptor causes phosphorylation and dimerization of receptor tyrosine kinase
3. Grb2, and adaptor with an SH2 domain, binds SOS (a GEF - guanine exchange factor). Grb2 then binds to phosphorlated domain of tyrosine kinase, which activates inactive Ras (GDP on Ras swapped out for GTP)
4. Active Ras activates MAPKKK
5. MAPKKK activates MAPKK which activates MAPK (MAPK is sometimes able to go into the nucleus to activate the gene target)
6. MAPK usually activates transcription activator (e.g. Jun) by phosphorylating it
7. Activated transcription factor enters the nucleus and binds DNA to activate transcription
146
Heterochromatin is (less/more) accessible to TFs
Less
147
What are 3 yeast telomeric sir (Silence Information Regulator) proteins? How do these proteins affect chromatin?
1. Rap1 protein (DNA-binding protein)
2. Sir2 protein (histone deacetylase)
3. Sir 3, 4 protein
Genes cannot be transcribed
148
What are three mechanisms to block the spreading of silenced regions?
1. Insulator elements can block the spread of histone modification
2. Histone methyltransferases may repress spreading of Sir2-mediated silencing
3. Methylation of histone H3 tail
149
Methylation of H3K4 on histone H3 tail (increases/decreases) transcription
Increases
150
Methylation of H3K9 on histone H3 tail (increases/decreases) transcription
Decreases
- Increases gene silencing
151
True or false: methylation of histone tails always suppresses expression
False
152
Genes can be silenced by methylation of which element of the genome?
Cytosines in CpG sequences
153
True or false: methylation of cytosines in CpG sequences completely turn off gene expression
False
- There is always some leakage
- Recruitment of other proteins can turn off gene completely
154
What allows for increases chromatin inaccessibility upon methylation of DNA?
Proteins (such as MeCP2) bind to the methylated DNA and recruit histone modifiers and nucleosome remodelers to completely turn off genes by making chromatin inaccessible
155
Define imprinting
Parental methylation of DNA determines gene expression in the offspring
156
What does imprinting ensure? Use insulin-like growth factor as an example
Imprinting ensures that only one parent's copy of Igf2 is active, while H19 is expressed from the other parent. This balance is crucial for normal development.
- On the maternal chromosome, the ICR is unmethylated, allowing the protein CTCF to bind. CTCF blocks the enhancer from activating Igf2. Instead, H19 is expressed, which is involved in non-coding RNA functions and suppressing cell division.
- On the paternal chromosome, the ICR and H19 gene are methylated, which silences H19 and blocks CTCF binding. This allows the enhancer to activate Igf2 expression, which promotes growth and development.
157
What is Beckwith-Wiedermann syndrome caused by? What does this result in, and what are some symptoms that the disorder is characterized by?
Excessive expression of paternal genes or a loss of maternal contribution of genes on chromosome 11
- Resulting in over-activity of the insulin-like growth factor 2 (Igf2) gene and/or no active copy of CDKN1C/H19 (an inhibitor of cell proliferation)
Characterized by:
- Overgrowth
- Enlarged tongue
- Midline abdominal wall defects (protrusion of umbilicus aka belly button)
- Severe hypoglycemia (low blood sugar after birth)
- Increased risk of childhood cancers
158
Describe how patterns of DNA methylation can be passed on through cell divisions
- CpG is palindromic, with the opposite strand also being CpG
- Upon DNA replication, hemimethylated CpGs are methylated by a maintenance methylase
CMMB 411
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