W4LECT - Epigenetics Flashcards
1
Q
What is epigenesis?
A
differentiation of cells from a totipotent state in embryonic development
2
Q
How do different adult stem cells know their fate?
A
- Myoblasts can only form muscle cells
- Hematopoetic cells only become blood cells
=> But all have identical DNA sequences.
3
Q
What is the reason of heterochormia?
A
An Individual Eye with Two Colors
4
Q
How can just paternal or maternal traits be expressed in offspring?
A
This is called genetic imprinting
5
Q
How can females express only one X chromosome per cell?
A
X inactivation
6
Q
How can acquired traits be passed on to offspring?
A
Some changes in gene expression that are, in fact, heritable!
7
Q
What is Epigenetics?
A
Changes in gene expression without altering the DNA sequence.
8
Q
What is the difference between GENETICS AND EPIGENETICS?
A
9
Q
Fill in the squares
A
- DNA
- DNA-methylation; Histone modification
10
Q
Fill in the squares
A
- Genetic code
- Epigenetic code
- Epigenome
11
Q
What are the 4 DNA Molecular Mechanisms that Mediate Epigenetic Phenomena?
A
- Transcriptional
- DNA methylation
- Histone modifications
- Chromatin remodelling
12
Q
DNA methylation
1. Describe DNA methylation
A
- Methylation of cytosin base
- Methylation with DNA Methyl-Transferase (DNMT) - General methyl donor (S-adenosyl methionine (SAM) - Change the binding ability of transcription factors
- Cytosine methylation maintains inactive-condensed chromatin state
13
Q
DNA methylation
2. Where does DNA methylation take place?
A
It takes place in CpG Islands !
14
Q
DNA methylation
3. Describe CpG islands
A
- Large number of CpG dinucleotide repeats
- Formal definition of CpG is a region with at least 200 bp, a GC percentage greater than 60% (av. 4-6%)
- p=phosphate
- 70% of promoters
contains CpG island - Promoters for functional noncoding RNAs such
as microRNAs
15
Q
What is the role of DNMT1?
A
Maintenance methylation
16
Q
What is happening here?
A
2nd round of replication:
-> passive demethylation
17
Q
What is happening here?
A
Denovo methylation
-> DNMT3A; DNMT3B
18
Q
What happen if there is deficiency in DNMT1, DNMT3A, DNMT3B?
A
DNMT1 - Embryonic lethal
DNMT3A: Perinatal death
DNMT3B: Embryonic lethal
19
Q
What are the 5 Effects and consequences of DNA methylation?
A
20
Q
Modification of Histones
1. Describe Modification of Histones?
A
These modifications alter the binding capacity of the transcription factors to the DNA through:
- Direct effect (charge distribution)
- Altering the secondary, - tertiary structure of the DNA
- Direct effect (charge distribution)
- Altering the secondary, - tertiary structure of the DNA
21
Q
Modification of Histones
2. What are the 6 main histone modifications?
A
- Acetylation /Deacetylation – of Lys (=K)
- Methylation – of Lys and Arg (= R)
- Phosphorylation – of Ser(S)
- Ubiquitination – Lys
- Biotinilation- Lys
- Citrulination/Deiminálás - Arg
(H3- tumorigenezis)
22
Q
Modification of Histones
3. Describe the enzymes that participate in Deacetylation/Acetylation of Histones?
A
- HDAC: Histone deacetylase deacetylation
-> positive charge
-> histone affinity to the DNA increases - HAT: Histone acetyltransferase
- Acetylation neutralizes the charge on lysines
-> histone affinity to the DNA decreases
23
Q
What is the histone code?
A
Different combinations of histone modifications, may be VERY SPECIFIC to the transcriptional state of the gene.
24
Q
What are the 3 parts of histone code?
A
- Erasers
- Writers
- Readers
25
Name the erasers of histone code?
1. Demethylases
2. Deacetylases
3. phosphatases
26
Name the writers of histone code?
1. Methyltransferase
2. Acetyltransferases
3. Kinase and ubiquitin ligase
27
Name the readers of histone code?
Bromo, chromo and Tudor domains
28
What is histone code hypothesis?
Different combinations of histone modifications, especially located near or within a gene’s promoter, may be VERY SPECIFIC to the transcriptional state of that gene.
29
Describe chromatin remodeling?
30
Fill in red squares
1. „Gene silencing”
2. „ Gene activation” - Transcription
31
How DNA methylation and histone modification interact and regulates the remodelling?
1. Histone H3-K9 methylation induces DNA methylation: repressed euchromatin + heterochromatin
2. DNA methylation induces Histone de-acetylation: repressed euchromatin + heterochromatin
32
Model of gene silencing
1. Fill in the squares
1. Methyl binding proteins bind to DNA
2. Recruiting deacetylase enzyme
3. Clearing acetyl groups from Lys
4. Firm connection between DNA and histones
33
Model of gene silencing
2. Fill in the squares
1. Methylation of H3 Lys9
2. Recruiting heterochromatine binding proteins
3. Compact chromatine structure
34
What is the role of DNA methylation and histone modifications ?
DNA methylation and histone modifications help to compartmentalize the genome into domains of different transcriptional potential
35
Describe DNA methylation and histone modifications in Euchromatin?
- High histone acetylation
- Low DNA methylation
- H3-K4 methylation
36
Describe DNA methylation and histone modifications in Heterochromatin?
- Low histone acetylation
- Dense DNA methylation
- H3-K9 methylation
37
What is epigenetic code?
Histone-code + DNA-methylation
38
What are the fields that Cytosin methylation is essential?
1. Gene expression
2. Chromosomal stability
3. Cell differentiation
4. Imprinting
5. X inactivation
6. Carcinogenesis
7. Aging
39
Describe DNA Methylation During Human Embryogenesis
1. DNA methylation is largely lost after fertilization, mostly from the paternal genome
2. Demethylation of the maternal genome continues until the blastocyst stage
3. DNA becomes remethylated upon differentiation
40
What are Epigenetic changes in identical twins?
1. Comparative monozygotic twins for methylated DNA
2. Yellow = similar pattern
3. Red = hypomethylated region in 1 twin compared to other
4. Green = hypermethylated region in 1 twin compared to other
41
What are Epigenetic changes during aging?
1. different histone variants
2. altered DNA methylation
3. altered histone modification
=> genomic instability, including DNA mutations
42
Comparison of the genome methylation in young and elderly
43
Explain aging in terms of epigenetic changes
- Measuring human ageing using epigenetic signals
- Developed a model that predicted a person's age from a saliva sample, the methylation state of about 353 cytosines.
-
44
What are the Factors may extend life spam?
1. STACs
2. Metformin
3. STACs
45
Factors may extend life spam
-> Identify
1. Metformin
2. STACs
3. Calorie restriction
46
Factors may extend life spam
-> Identify
1. Rapamycin
2. Spermidine
3. Acetyl CoA depletion
47
Describe Anti aging therapy
- It is widely prescribed antihyperglycemic agent
- Growing evidence for anti aging and anti cancer effect by the induced chromatin remodelling
- The main problem of therapies inducing epigenetic changes: lack of specificity and tissue- dependent target
48
Describe differences between histone modifications in mortal cells and that in cancer cells
1. Hypermethylation of CpG islands in the promoters of tumor suppressor genes are methylated
=>Tumor suppressor genes are inactivated
2. General Hypomethylation (e.g. Line) => Genome instability
49
What are RNA Molecular Mechanisms that Mediate Epigenetic Phenomena
- Post Transcriptional
- Non coding RNAs
+) miRNA
+) siRNA
+) lncRNA
50
What are the Types of non-coding RNAs?
1. Long ncRNA
> 200 b
2. Short ncRNA
< 200 b
- siRNA
- miRNA
51
'Central dogma’ and aspects of non- coding RNAs functions
-> Identify
1. Chromatin modifications
2. Poll activity regulation
3. Transcriptional interference
52
What is the acting mechanism of Long-non cooding RNS?
1. Epigenetic controll
2. cardiomyocyte differentiation
3. Inhibition of the odontoblast differentation in dental pulp
53
What is the role of miRNAs?
- Regulate gene expression via post- transcriptional repression;
- Evoking messenger RNA (mRNA) degradation or translational repression
54
What are the Molecular Mechanisms that Mediate Epigenetic Phenomena in case of protein
- Post Translational
- DNA remodelling
(histone modification)
55
X-inactivation (Lyonization) in mammalian females
-> Identify
Barr-body
56
Describe Dosage compensation
X chromosome inactivation in females (randome)
57
Describe XIST
(X-inactive specific transcript)
1. 17 kb spliced, non-coding RNA
2. Stable expression only from inactive X
3. ”Paints” inactive X chromosome
4. Required to initiate silencing
58
Describe Mammalian X-chromosome inactivation
1. X-chromosome inactivation begins with the synthesis of XIST (X-inactivation specific transcript) RNA from the XIC (X-inactivation center) locus.
2. The association of XIST RNA with the X chromosome is correlated with the condensation of the chromosome.
59
What are the 3 types of X chromosome inactivation and their consequences?
1. Random XCI
=> Both normal and mutant product made
2. Skewed XCI ’fortunate’
=> Makes mostly normal product
3. Skewed XCI ’unfortunate’
=> Makes mostly mutant product
60
Describe Hypohydrotic ectodermal dysplasia
61
Describe Skewed inactivation
1. Skewed inactivation modifies the expressivity of X-linked inheritance
- e.g. Hypohydrotic ectodermal dysplasia
2. Areas without sweat glands are shown in green in heterozygotes.
62
What is Genomic imprinting?
the non-equivalent expression of genes based on parent-of-origin
63
NUCLEAR TRANSPLANTATION DEMONSTRATES THE NON-EQUIVALENCE OF PARENTAL GENOMES
=> What are the consequences of these things?
64
What are the difference between maternal imprinting and paternal imprinting?
1. Maternal imprinting
- limits use of maternal resources by baby in utero
- „Growth” genes silenced in maternal chromosome
2. Paternal imprinting
- maximizes use of maternal resources by baby in utero
- „Growth inhibitory” genes silenced in paternal chromosome
65
Give 2 examples of disease related to genomic imprinting
1. Angelmann syndrome (AS)
2. Prader-Willi syndrome (PS)
66
Give 2 examples of disease related to genomic imprinting
1. Angelmann syndrome (AS)
2. Prader-Willi syndrome (PS)
67
What are the symptoms and imprinted genes suspected or known to be affected of Angelmann Syndrome?
1. Symptoms:
- Severe motor and mental retardation
- Paroxysms of laughter
- Autistic-like behavior
2. imprinted genes suspected or known to be affected:
UBE3A: Ubiquitin ligase regulates the release of glutamate receptors in the synapse
3. expressed gene copy: maternal
68
What are the symptoms, expressed gene copy and imprinted genes suspected or known to be affected of Prader-Willi Syndrome?
1. Symtomps:
- Moderate mental retardation
- Severe obesity
- short stature
- Poor muscle tone
2. Numerous imprinted genes in chromosome 15
3. expressed gene copy: paternal
69
What are the characteristics of Human Epigenome Project (HEP)?
1. Epigenomics Road Map (2008-Present)
― Goal: Create map of epigenome in multiple tissue types and cancers
2. The human genome is the musical score of human existence, but the human epigenome is the conductor.
70
Describe Epigenetics in dentristry
71
What is Epigenetics?
Epigenetics is the study of heritable mechanisms that affect the transcriptional state of a gene, and generally lead to
monoallelic expression of that gene.
72
Summary of epigenetics
-> Patterns of (1)____ in adult cells (2)____, chromatin structure and gene activation.
1. DNA methylation
2. parallels cell fate
73
Summary of epigenetics
-> Most ____ and re-established during embryogenesis.
DNA methylation is removed at fertilization
74
Summary of epigenetics
- (1)____ keep their (2)_____ giving rise to parental patterns of expression.
1. Imprinted genes
2. parental pattern of methylation
75
Summary of epigenetics
- Patterns of ___ parallel DNA methylation.
histone modifications
76
Summary of epigenetics
- (1)____ and distinctive histone
modifications ((2)____).
1. Active gene regions have little DNA methylation
2. acetyl groups and H3K4methyl
77
Summary of epigenetics
- X chromosome inactivation in females is correlated with ___ on one chromosome, condensation, inactivation and Barr body formation.
extensive CG island methylation
78
Summary of epigenetics
- Alterations in gene and ___ patterns are seen in aging and in cancer.
CpG island methylation
79
___ is unmethylated in 93% of inflamed pulp tissue samples
Interferon gamma gene
