Hipfner Flashcards
(183 cards)
1
Q
How is prokaryotic transcription different from eukaryotic?
A
-No nucleus (t+ t can occur simulatneously)
-DNA not wound in nucleosomes
-Intronless
2
Q
Operons?
A
Genes encoding enzymes involved in the same metabolic process are often organized in operons (located next to one another in the chromosome, co-transcribed in a single mRNA from a single transcription initiation event)
-One mRNA encoding muliple proteins
3
Q
+1
A
Transcription start site
4
Q
Promtoer?
A
Trnascription initiator
5
Q
Sigma factor of RNA polymerase?
A
Binds to -35/-10 promoter sequences to properly position the holoenzyme at the start site
6
Q
How does the RNA polymerase find the promoter?
A
Binds the DNA transiently then scans along DNA until it reaches the promoter
7
Q
Preferred sugar to be metabolized by bacteria?
A
GLucose
8
Q
Transcription Factors?
A
have a sequence specific DNA binding domain, that allows them to interact with regulatory DNA sequences located just upstream of the bacterial genes
9
Q
Activators?
A
Bind a region upstream of the promoter and facilitates the binding of RNA polymerase to DNA
10
Q
Repressors?
A
bind to the operator and blocks RNA polymerase from binding to the promoter
11
Q
How prokaryotic genes are transcribed?
A
Transcription of genes is initiated when RNA polymerase binds to the promoter sequence(just upstream of the transcription start site)
Ability to bind to the promoter can be enhanced by transcription activators binding to sequences near the promoter and positively regulating transcription
Ability to bind the promoter can be repressed by transcription repressors which prevent RNA polymerase from transcribing the gene, negatively regulating gene expression
12
Q
How are transcriptional activators/repressors regulated?
A
Through allosteric regulation
13
Q
Allosteric site?
A
Region on the protein that binds the effector, when bound there is a conformational change
14
Q
Allosteric regulation of an activator?
A
Effector bound: conformational change of active site can bind DNA promote transcription
Effector unbound: Activator unable to bind DNA transcription levels are basal
15
Q
Allosteric regulation of a repressor?
A
Effect bound: conformational change cannot bind DNA, basal transcription
Effector unbound: Repressor is able to bind to DNA and reduce transcription of the genes (negative regulation)
16
Q
Inducer
A
An molecule that binds allosteric site of activator inducing transcription and when bound to repressor induces transcription
17
Q
Describe the genes of the Lac operon?
A
-LacZ: b-galatosidase
-Lac permease
-LacY: allows lactose to enter bacteria
18
Q
Describe the lac operon?
A
-Promoter
-Downstream of the promoter there is a operator that the repressor can bind to
19
Q
LacI
A
Lac Operon repressor protein that blocks transcription when unbound by lactose
Transcribed on a separate gene
20
Q
Describe the Lac Operon in the absence of Lactose
A
- No lactose binds to repressor, repressor binds to the operator and prevents RNA polymerase from being able to transcribe the LacZ, LacY and permease genes
Negative regulation
21
Q
Describe the Lac Operon in the presence of lactose?
A
- Lactose binds to the repressor preventing it from binding to the operator.
- RNA polymerase can now bind to promoter and start transcription
22
Q
Uniducible?
A
When both genes cannot be turned on even in the presence of an activtor
23
Q
Constitutive
A
When both genes cannot be turned off even the presence of a respressor
24
Q
Partial Diploids?
A
When bacteria have two copies of the lac operon: one on the chromosome and one on a plasmid
But don’t have a second copy of any other genees
25
Why do we use partial diploids?
To test whether mutations are dominant/recessive and if elements are cis-acting or trans-acting
26
Cis vs Trans?
Cis: Cis-acting elements only affect genes on the same DNA molecule
Trans: Trans-acting elements can diffuse and act on both copies
27
Mutant P vs Wild type P
Mutant P: production of the enzymes is uninducible
Wild-type P: production of the enzymes is inducible
28
P mutated in the plasmid copy along with lacZ and Y, but wild type in the endogenous copy?
Inducible because endogenous is wild-type for all
29
P-Z+Y+/P+Z-Y-
Uninducible. This means that the promoter is a cis-acting element
30
O+Z+Y+
Inducible
31
O^CZ+Y+
Constitutive, repressor cannot bind
32
O+Z-Y+/O^CZ+Y+
Constitutive
33
O+Z+Y+/O^cZ-Y-
Inducible, this proves that the operator is cis-acting because it did not cause constitutive transcription in the endogenous genes
34
I+Z+Y+
Inducible
35
I-Z+Y+
Constitutive
36
I+Z-Y-/I-Z+Y+
Inducible, this indicates that the repressor protein is trans-acting and can act on all operators
37
Super-repressor mutation in I(IS)
Mutation that causes the repressor protein to be constantly bound to the operator repressing transcription (uninducible)
38
ISZ+Y+/I+Z+Y+
Uninducible, this means that IS is dominant to I+ and trans-acting
39
Positive regulation of the lac operon in high levels of glucose?
No cAMP is produce and CAP cannot be activated and transcritption of the lac operon is reduced
40
Positive regulation of the lac operon in low levels of glucose?
cAMP is produced, cAMP binds to CAP to form cAMP-CAP complex that binds the promoter just upstream of RNA pol and facilitates the recruitment of RNApol to P
41
Glucose present but no lactose?
No lactose: Repressor can bind operator and lowers transcription of the lac genes
(negative regulation)
Glucose: Low level of cAMP, no activation of CAP(no increase in transcription of lac genes)
42
Glucose present and lactose present?
Lactose binds the repressor unable to bind(increases transcription)
Glucose present= low cAMP, no activation of CAP)
43
No glucose and lactose present?
Lactose: binds repressor preventing binding to operator(increases transcriptioN)
Glucsose: no glucose so cAMP levels are high and it bind CAP and binds the promoter increasing transcription
44
RNA polymerase?
moves along the DNA template strand in the 3’ to 5’ direction, forming phosphodiester bonds that covalently link aligned ribonucleotides to build RNA in the 5’ to 3’ direction
45
How does the same RNA polymerase bind to many different promoters of various genes?
Promoter regions in genes must contain similar sequences specifically -35 and -10 regions that are similar
46
How does RNA polymerase bind to the promoter?
RNA polymerase recognizes the consensus sequence at -35/-10 and then RNA holoenzyme binds and unwinds the DNA double helix
47
RNA polymerase holoenzyme?
Contains the sigma factor which is the region that finds the -35/-10 consensus sequence. Once transcription initiates it dissociates
48
Upstream vs Downstream of the initiation site
Upstream: negative(-)
Downstream: positive (+)
Initiation site/first DNA base to be transcribed: +1
49
Protein encoding region of the gene?
Begins with an AUG sequence in the mRNA
The transcription start site is usually upstream of the beginning of the gene encoding region
The region between the transcription start site and gene encoding region = 5’ UTR
50
3'UTR?
Transcription continues beyond the protein-coding segment of a gene which creates the 3' UTR at the end of the mRNA transcript
51
Binding site for repressors?
Operators
52
Postive vs Negative regulation
Positive: Presence of a bound activator is necessary for transcription
Negative: Regulation mediated by factors that block or turn off transcription, absence of the repressor allows for transcription
53
How do activators promote transcription?
bind to DNA and often help tether RNA polymerase to its nearby promoter so that it can begin transcribing
54
How do repressors inhibit transcription?
bind to DNA and can either physically interfere with the binding of RNA polymerase to its promoter or can impede the movement of RNA polymerase along the DNA chain
55
T/F: Both activators and repressors must be able to recognize when environmental conditions are appropriate for their actions?
True
56
What makes up the lac operon?
P, O, Z and Y
57
T/F: The lacI gene is not considered part of the lac operon itself ?
True
58
How does CAP-cAMP increase transcription?
CAP binds to specific DNA sequences of the lac operon and can interact physically with RNA polymerase and increase the enzymes' affinity for the lac promoter
59
Four ways transcription in eukaryotes is more complex than prokaryotes?
1. Eukaryotes have many genes that are spaced far apart
2. Eukaryotes have three RNA polymerases
3. Transcription in eukaryotes takes place in the nucleus
4. DNA in eukaryotes in packaged with proteins into chromatin
60
RNA pol I?
Transcribes rRNAs
61
RNA pol II?
Trnascribes all mRNAs and some ncRNAs including snRNAs and miRNAs
62
RNA pol III?
Transcribes tRNAs, 5s rRNA and some snRNAs
63
General transcription facotrs?
Each RNA polymerase requires a set of GTFs in order to bind to promoters and initiate transcription. These bind to the promoters and then recruit RNA pol
64
Nucleus in eukaryotes?
Separates transcription and translation
65
How do GTFs know where to bind?
DNA sequences located near the transcription start site are consensus sequences
66
rRNA gene transcription?
rDNA genes reside in the nucleolus and this is also where transcripts are synthesized. Each rRNA transcript contains 18S, 5.8S and 28S rRNAs and spacer regions. After transcriptio, spacer are spliced out and 60S ribosomal subunit is assmebled
67
Promoter elements in rDNA genes?
TATA-binding protein
Upstream control element bound by the upstream binding factor
68
RNA polymerase II promoters?
Located within 100bp of the TSS
25% of the promoters contain TATA box located 30 bp upstream of TSS
69
Additonal promoter elements ?
-Initiator(located at the TSS)
-DPE (+25)
-BRE recognized by TFIIB(-40)
70
What binds to the TATA box?
TFIID which has a TBP domain
71
RNA polymerase transcription initiation?
1. TFIID binds to promoter sequences.
2. TFIID recruits TFIIA and TFIIB, followed by TFIIF and RNA polymerase
3. TFIIE and TFIIH then bind
72
TFIIA?
stabalizes binding of TFIIB and TFIID at the promoter
73
TFIIH?
ecruitd to the promoter by TFIIE contain proteins with helicase activity that unwind the DNA to form the transcription bubble
74
TFIIF?
places the promoter DNA in a position in RNA polymerase II that is appropriate for DNA unwinding and initiation of transcription at the start site
75
RNA polymerase II transcription elongation
RNA polymerase II is phosphorylated by a protein kinase in the TFIIH, this helps start processing mRNAs as they are being transcribed
The CTD of the RNA pol II contains the sequence YSPTSPS tandemly repeated 26 times in yeast and 52 in humans. Phosphorylation of serine in position 5 by TFIIH serves as a signal for the binding of enzymes that cap the 5’ end of the mRNA
76
Nucleosomes
DNA is bundled into nucleosomes in eukaryotes which must be loosened in order for transcription factors to bind/work
Nucleosomes are composed of histone proteins and help keep gene expression “off”
77
Transcription factors?
bind directly to regulatory DNA sequences called enhancers
78
Proximal enhancers?
enhancers located close to the core promoter and are part of the proximal promoter
79
Distal enhancers?
enhancers located a considerable distance from the promoter
80
Core promoter?
Region of eukaryotic promoter that contain the transcription start site, often defined as -50 to +50
81
Coregulators?
do not directly bind to DNA
82
Coactivators?
increase the amount of transcription through binding or enzymatically modifying other transcription regulatory factors
83
Corepressors?
decrease the amount of transcription through binding or enzymatically modifying other transcription regulatory factors
84
T/F:Point mutations in proximal enhancers and core promoters reduces transcription of a gene
?
True
85
Enhancers?
-short sequence elements
-Frequently occur as inverted repeats of the same DNA sequence for binding of two similar or identical transcription factors
-Occurs randomly many times in the genome since they are short
86
ALL transcription factors contain a DNA-binding domain and an activation/repression domain, but only some TFs contain dimerization and ligand-binding domains
Yes
87
Genes used to create enzymes that metabolize galactose in yeast?
GAL1, GAL2, GAL7, GAL10
88
Genes that encode proteins that regulate the enzyme-encoding genes of galactose?
GAL3, GAL4, GAL80
89
GAL4
-key regulator of gene transcription is the GAL4 transcription factor that directly binds sequence specific DNA
90
Mutations in GAL4?
GAL4 mutations the GAL1, GAL2, GAL7 and GAL10 genes are not expressed in the presence of glucose this means GAL4 must be required for transcription of these genes
91
Describe where GAL4 is found?
Each of the four genes has two or more Gal4-binding sites(enhancers) located at some distance 5’(upstream) of its promoter
92
GAL10 and GAL1 where is GAL4?
These genes are adjacent and transcribed in opposite directions. Between the two genes’ transcription start sites is a 118 base pair region that contains four Gal4-binding sites.
93
Deletion of GAL4 binding sites?
GAL genes are transcriptonally silent
94
ANother name for the GAL4 enhancers?
Upstream activation sequence
95
GAL4 domains?
-DNA-binding domain
-DImerization domain
-Activation domain
96
How did reasearchers learn that DNA-binding domain and activation domain of GAL4 are independent?
1. Created a fusion protein with LexA DNA-binding domain + GAL4 activation domain
2. Reporter genes contain LexA-binding sites or GAL4 UAS upstream of LacZ
3. Only fusions that had both a DNA-binding domain and activation domain could drive transcription
Proved independence because DNA-binding domain along could bind DNA but did not activate transcription and activation domain alon had no effect cause it could not bind DNA
When the proteins were fused activation was preserved even when attached to a completely different DNA-binding domain
97
GAL4?
Is an activator that binds DNA at the UAS always and its activation domain drives transcription only when free of Gal80
98
Gal80?
Repressor(co-respressor)
Binds to the activation domain of Gal4 to inhibit it .
Always present unless inactivated
99
Gal3?
Sensor + inducer
Binds galactose + ATP< changes shape, and sequesters Gal80 activating transcription
100
Gal80 mutant?
Can't repress Gal4 which leads to constitutive transcription even without galactose
101
Gal3 mutant?
Can't sense galactose, Gal80 remains bound to Gal4, no transcription even with galactose
102
Regulation of Lac operon vs the GAL system?
Lac: DNA binding of LacI is regulated
GAL: Activation domain activity of Gal4 is regulated
103
Chromatin?
DNA + Histones
Compacts DNA so that it can fit inside the nucleus
104
Chromatin compaction?
-Wrapping of DNA around histone octamers forms a structure of around 11nm in diamete
-To achieve this higher order of compaction, nucleosomes fold upon themselves the next order of compaction produces a structure that is around 30nm in diameter
105
Compaction of nucleosomes during mitosis vs interphase?
Mitosis: highly compacted
Interphase: less compacted
106
Constitutive heterochromatin?
Typically found at centromeres, telomeres and region rich in repetitive sequences and poor in gene
107
Heterochromatin vs Euchromatin?
H: More compacted regions of DNA
E: less compacted regions of DNA
108
Facultative heterochromatin?
Does not remain as heterochormatin throughout the cell cycle
109
Gene-dense chromsomes ve Gene-poor chromosomes locations?
Dense: located near the centre of the nucleus
Poor: located near the nuclear periphery
110
Topologically Associating Domains(TADs)?
Large regions of the genome spatially organized within the nucleus
Within a TAD, regions of DNA are more likely to interact with each other than other regions outside the TAD plays a crucial role in gene expression
111
Function of TADs?
Serve to bring together distant parts of the genome, such a enhancers and promoters ensuring coordinated transcription
Also help to restrict interactions between different regulatory elements
112
Insulators?
DNA elements that act as barriers to prevent interactions between adjacent TADs, ensure only appropriate enhancer-promoter interactions occur
113
Two major mechanisms in eukaryotic cells enable dynamic access of the transcription machinery to DNA?
1. Chromatin modification
2. Chromatin remodeling
114
Chromatin modification?
Enzymes alter the chemical structure of amino acids in histone or nucleotides in DNA to affect recruitment of TFs, coregulators and GTFs
115
Chromatin remodelling?
Accessibility of DNA to TFs, coregulators and GTFs is altered by enzymes that use ATP hydrolysis to remodel the nucleosomes
116
Histone acetylation?
Type of chromatin modification
- addition of an acetyl group to the amino group of a lysine amino acid side chain this neutralizes the positive charge of lysine preventing interaction with DNA backbone
117
Lysine Deacetylation?
Chromatin modification that increases compaction of chromatin and reduces accessibility of the transcription machinery to DNA
118
Histone acetyltranserase(HAT)?
Enzyme that transfers an acetyl group from acetyl CoA to lysines in histones
Transcription coactivator
119
Histone deacetylases(HDACs)?
An enzyme that removes acetyl groups from lysines in histones
Transcription corepressor
120
Methylation?
Can occur to Lysine or arginine
-HMTs, HDMs
121
Phosphorylation?
Serine or threonine or tyrosine
122
Ubiquitintation ?
Lysine
123
Histone Code Hypothesis?
Multiple histone modifications, act sequentially or in combination on one or several histone tails to specify unique transcription outcomes
124
Evidence of the histone code?
Methylations on lysine 4 (H3K4me3) activates transcription by serving as a binding site for transcription coactivators
Methlations on lysine 9(H3K9me3) repress transcription by serving as a binding site for co-repressors
125
DNA modification: Chromatin modification?
DNA methylation occurs at cytosine bases in CpG nucleotides by DNMT and represses transcription
126
CpG islands?
Unmethylated CpG regions of the genome found in gene promoters, intragenic/intergenic regions
Associated with active transcription
127
SWI/SNF remodelling complex
Remodels the nucleosome by removing dimer histone proteins and histone octamers out of the wat
128
Epigentic inheritance ?
Heritable modifications in gene function that do not change the DNA (ex. Histone modifications are heritable)
Effects the traits of daughter cells without altering DNA sequence
129
Four ways of epigenetic control of transcription?
Cellular memory
Position-effect variegation
Genomic imprinting
X-chromosome inactivation
130
Polycomb proteins?
maintain genes in a transcriptionally repressed
131
Trithorax proteins?
maintain genes in a transcriptionally active state
132
How do trithorax and polycomb proteins work?
Polycomb complex trimethylates H3K24(histone modification associated in transcription silencing), while a Trithorax complex acetylates H3K27 (associated with transcription activation)
133
Position-Effect variegation?
Flies were irradiated with X rays to induce mutations in their germ cells, and progeny of irradiated flies were screened for unusual phenotypes
Among the mutants, flies were found that had eyes with patches of red and white colour. This is unusual because typically wild-type flies have uniform red eyes, and flies that are mutant for the white gene, which is required for the red pigments have uniform white eyes.
134
What was wrong with the eyes with patches?
In mutant flies a region of the X chromosome containing the white gene was inverted
135
Inversion of the white gene?
The white gene, which is normally located in an euchromatic region of the X chromosome, now is near the heterochromatic centromere
The patchy eye phenotype is due to spreading of heterochromatin into the wild-type white gene and silencing of white transcription in some cells but not others
136
White patches vs Red in the mutant fly?
Patches of white were derived from descendants of a single cell in which the white gene is silenced and remains silenced through future cell divisions due to spreading of heterochromatin
Patches of red arise from a cell in which heterochromatin has not spread into the white gene, and so the white gene remains active in all its descendants
137
The two epigenetic transcription regulation mechanisms seen in the patchy eye?
1.Differences in chromatin structure across chromosomes can be inherited from one cell generation to the next
2. Different in chromatin structure across chromosomes affect expression of resident genes
138
Position effect variegation?
Variation in a phenotype among cells within a tissue due to transcriptional silencing of a gene in some cells through its juxtaposition with heterochromatin
139
Suppressor of varigation(Su(var)?
A gene that when mutated reduces the spread of heterochromatin, meaning that the wild-type product of this gene is required for spreading.
140
Enhancer of variegation(E(var))?
a gene that when mutated increases the spread of heterochromatin and normally functions to block spreading.
141
Boundary/insulator elements and PEV?
-Prevent spreading of heterochromatin by creating a local environment that is not favorable to heterochromatin formation
nsultor-binding proteins may block the spread of heterochromatin by recruiting activating enzymes such as histone acetyltransferases, H3K4 methyltransferases, and SWI/SNF chromatin remodels, or they may block access to histone by directly bind the
142
What is gene imprinting?
Certain autosomal genes are expressed in a parent-of-origin-specific manner
143
Maternal Imprinting?
Copy of the gene derived from the mother is transcriptionally inactive
144
Paternal Imprinting?
The father’s allele is transcriptionally silenced.
145
Imprinting control regions?
these are regulatory elements in the DNA that control imprinted genes
146
Igf2-H19 cluster?
These genes contain an ICR between them that is methylated in male germ cells and unmethylated in female germ cells.
147
Igf2-H19 cluster in male germ cells?
ICR is methylated and cannot bind CTCF and the enhancer can activate Igf2 transcription. However, the enhancer cannot activate H19 because the methylated region extends into the H19 promoter
148
Igf2-H19 cluster in female germ cells?
The unmethylated ICR can be bound by CTCF which acts as an enhancer blocking insultator that prevents activation of Igf2 transcription. However, H19 is transcribed
149
Disease inheritance and parental imprinting?
imprinted genes are essentially haploid because only one of the two copies is expressed
Diseases in imprinted genes occur due to mutations in the non-imprinted, transcriptionally active copy of imprinted genes
150
Dosage compensation in female X-chromsomes?
Females have two copies of the X chromosomes and male have only one, creating a potential imbalance in transcription of genes residing on the X chromosome. This imbalance is corrected by transcriptional silencing of one of the two X chromosomes in females through a process called X-chromosome inactivation
151
Barr-body ?
Silenced X-chromosome in the nucleus
Heterochromatic
Inactivation of the X chromsome is random, but all daughter cells will have the same X-chromosome inactivated
152
How is the X-chromosome inactivated?
1. Early in development of the embryo both X chromosome are active, Tsix is expressed from both alleles
2. At the beginning of X chromosome inactivation, transient pairing of the X chromosomes represses transcription of Tsix from one allele, establishing the future inactive X chromosome
3. Transcription from the other allele blocks transcription activation of Xist
4. Xist RNA spreads along the future inactivated chromosome and induces silencing, as it spreads Xist recruits polycomb repressive complex 2 to repress transcription
153
Extranuclear inheritance?
A subset of genome found inthe mitochondria that are inherited independently of the nuclear genome(non-mendelian)
154
Chloroplasts and Mitochondria?
Each organelle is present in many copies in the cell and each organelle contains many copies of its chromosome
155
T/F: A eukaryotic cell can contain hundreds or thousands of organelle chromosomes ?
True
156
Nucleoids?
Suborganellar structures which mitochondrial and chloroplast DNA can be packaged within
Can contain introns
157
Uniparental inheritance?
Seen in organelle genes, this is when progeny inherit organelle genes exclusively from one parent but not the other
158
Maternal Inheritance?
Organelle chromosomes are located in the cytoplasm of the cell and the male and female gametes do not contribue the same amount of cytoplasm.
The egg contributes the bulk of the cytoplasm. No organelle DNA comes from the father
159
Heteroplasmons?
When the cell contains a mixture of both mutant and normal organelles
160
What happens in heteroplasmons?
Oftentimes, the mutant and wild-type mitochondria segregate over successive cell divisions and sort themselves into separate cells, yielding mutant cells and wild-type cells
161
How can a pure mutant cell be created?
A variant will arise by mutation of a single-gene in a single chromosome. The mutation-bearing chromosome may by chance increase in frequency in the population within the cell(random genetic drift). A cell may have 60% wild-type chromosomes and 40% mutant chromosomes. When this cell divides, sometimes all of the mutant chromosomes segregate together and all of the wild-type chromosomes segregate together(by chance). This often requires several generations of cell division. These two alleles are now expressed in different daughter cells and the continual division will lead to one completely mutant cell.
162
How can we identify cytoplasmic mutations in pedigrees?
When diseases are transmitted only through females and never through males
163
How to identify enhancers?
Take your suspected enhancer and place it upstream of a promoter and gene in the reporter gene significantly increases transcription it is most likely an enhancer
164
HMTase?
Histone methyltransferase enzymes add the methyl group
-Does not affect charge
Depending on where they can be markers for silencing or activation
165
Barrier insulators?
stop the spread of chromatin so that our entire genome does not become heterochromatin
Barrier insulators are DNA sequences that get bound by HATs which then cause the acetylation of the histone and formation of euchromatin instead of heterochromatin
Barrier insulators exist at particular sequences in the genome and prevent the spontaneous spread of heterochromatin
166
Wild type X chromosome Red eyed flies?
Centromeric region is heterochromatic
White gene is in the middle of the telomeric region which is euchromatic, so white gene is able to be expressed
There is a barrier insulatior between the heterochromatic region and the euchromatic region which is preventing the telomeric region from becoming heterochromatic
167
Red patches on flies?
Inversion causes some cells where the white gene is near the heterochromatic region the barrier insulator stays near the heterochromatic region and prevents the white gene from being turned into heterochromatin and not being transcribed
168
White patches on flies?
The inversion of the gene causes the barrier insulator region to move to where the white gene originally was and now the white gene which is where the barrier insulator was is now turned into heterochromatin and is unable to be transcribed
169
Examples of E(var)?
Mutated HATs made spreading increase, since wild-type HATs normally decreasing spreading by acetylation which leads to euchromatin
170
Example of S(var)?
Mutated HMTs and HP-1 both made spreading decreasing, since wild-type HMTs cause methylation which increases heterochromatin and HP-1 increase heterochromatin spreading
171
Methylation of H3K4?
H3K4me is recognized by HP-1 (heterochromatin protein 1) and binds to it
HP-1 promotes heterochromatin formation and recruits additional HMTase enzymes
HMTase enzymes then methylate the neighbouring nucleosomes
The neighbouring nucleosome will then continue this process starting at 1, which will cause the heterochromatin formation to spread down the length of the chromatin
172
Non-mendelian inheritance of some X-linked diseases(skeweked X inactivation)?
For many X-linked mutations female carriers(heterozygotes) can display “partial” symptoms with variable penetrance and expressivity due to “skewed X inactivation”
Skewed X inactivation: Instead of the expected 50/50 inactivation of maternal vs paternal X chromosomes sometimes a female will inactivate more paternal or more maternal X-chromosomes
173
Red and Green colour blindness is the result of a mutation in the OPN1-LW gene on chromosome X desrcribe males vs females arising from this?
Males: mut/Y (colourblind)
Females: mut/+
- 50/50 X-inactivation ; have cells are wild type = not colour blind
- Skewed X-inactivation: Majority of cells inactivated the wild-type X chromosome which now results in more color-blind mutant cells and results in red-green color blindness
174
Rett Syndrome?
An X-linked disease only seen in females because mut/Y males are not viable
175
How is the inactivated X in humans silenced?
Increase histone methylation
Decrease in histone acetylation
DNA methylation
176
Methylated CpG islands?
Direct effect: prevents transcription by preventing TF from binding to DNA
Indirect effect: Recruits HDACs and HMTs that further repress the gene by methylating the histones and removing the acetylations
177
How are DNA methylation modification passed on through mitosis?
1. After the new strands of DNA are transcribed and half of them are methylated (hemimethylated), DNMTs come in to methylate the newly synthesized strands lacking the methylation
2. DNMTs have a high affinity for hemimethylated sites and help to reestablish the methylation marks on newly synthesized strands
178
Igf2 knockout?
Igf2: maternally imprinted
Mutant father = mutant pups
Wild-type mother/mutant mother = does not mater
179
How is the imprinted copy inactivated?
Imprinted copy is inactivated by a mechanism involving DNA methylation in the maternal or paternal germline. The meyhtlation imprint is maintained through lifeof the progeny in somatic cells
180
T/F: Imprints are established during gametogenesis (process cells undergo to produce gametes)?
True
181
Gametogenesis H19 and Igf2 ?
1. Male and female cells start with one methylated copy of a chromosome from their father and one unmethylated copy from their mother.
2. The DNA methylation of both male and female chromosomes is removed in the primordial germ cells
3. DNMTs present only in male primordial germ cells will methylate the ICRs in both male chromosomes. In females, there are no DNMTs and thus no methylation occurs.
4. Then the gametes form. All male gametes have methylated ICR regions and all female gametes are unmethylated.
5. Now when fertilization occurs the offspring will have one methylated copy of the chromosome and one unmethylated copy.
182
Paternal Allele ?
Sex-specific methylation of the ICR region occurs in males and this spreads to the CpG islands near the promoter of H19. This prevents TF from binding to the promoter and leads to inactivation of the H19 gene in the paternal allele.
The methylated ICR is unable to bind CTCF, so now the enhancer can act on the Igf2 gene and enable its expression
183
Epigenetics and cloning?
Cloned animals are formed from cells not made in the germline which means they lack epigenetic marks
The lack of epigenetic marks leads to cloned animals being less healthy and more likely to die compared to animals produced via the germline
