FINAL EXAM EPIGENETICS
Among all epigenetic mechanisms, which one seems the most relevant for dosage compensation in mammals? -RNA interference -Histone variants -Histone PTMs -DNA methylation
A
As discussed in class, the term pleiotropic effect: -Refers to the capacity of some drugs to affect multiple different mechanisms. -Refers to the result of methylation in up-regulation of certain genes. -Refers to cancer treatments involving combinatorial therapies of different drugs. -Refers to resistance to certain cancer treatments after prolonged use.
A
Azacitidine and decitabine are examples of: -Hypomethylating agents -Hypermethylating agents -Deacetylating agents -Chromatin remodeling agents
A
Epigenetic marks are less stable in what kinds of cells? -Totipotent and pluripotent cells -Somatic and germinal cells -Older cells -Multipotent cells
A
Histone deacetylation of an oncogene will most likely: -Decrease the likelihood of abnormal gene expression since chromation would become compacted and inaccessible to transcription factors. -Result in abnormal upregulation of the gene, most likely leading to cancer -Increase the chances of tumorigenesis if certain environmental factors come into place -Ensure that the gene will never be expressed and thus decrease the likelihood of cancer.
A
In the absence of recombination, what would be the fate of the Y chromosome and sex reproduction in humans? A.Elimination of Y chromosome and the end of sexual reproduction in humans as we know it. B.Differentiation of Y into other type of chromosome without consequences for sexual reproduction in humans. C.Elimination of Y chromosome and the end of sexual reproduction in humans as we know it. D. The lack of recombination will not impact the evolution of the Y chromosome.
A
What is genomic imprinting? -Preferential expression or repression of one of the parental genes. -An epigenetic modification that occurs in babies due to environmental conditions at time of birth. -Random silencing of one allele so that only allele is expressed. -When baby ducks hatch and become attached to the first thing they see.
A
What type of genes would you expect to be expressed on the chromosome below? -Non imprinted genes only -Imprinted genes only -Al types of genes -No genes expressed
A
Which experimental result provides evidence for environmental memory in corals? -Corals that were rotated in 2000 (so that western sides instead faced east) bleached less than control corals in a 2010 thermal bleaching event -Pocillopora damicornis corals had significantly different metabolism and higher % DNA methylation after exposure to high temperature and high CO2 conditions -After 6 weeks of exposure to high temperature and high CO2 conditions, Montipora capitate corals had no significant differences in growth rate or % DNA methylation -In corals, highly methylated genes are often highly expressed, housekeeping genes
A
Which is not necessary for the transgenerational epigenetic inheritance of environmentally-induced epigenetic marks? -Epigenetic marks must be reversible in the absence of the environmental cue -Epigenetic marks must endure chromatin reorganization during gametogenesis -Epigenetic marks must escape epigenetic reprogramming during embryogenesis -Epigenetic marks must be incorporated into germ cells
A
Which of the following is an important consideration when designing a study to test for transgenerational epigenetic inheritance? A.All answers are correct. B.social transmission of environmental information C.matrilineal vs. patrilineal breeding designs D.genotypic diversity of the study organisms
A
Which of the following is not a conclusion that can be drawn from the study exposing two coral species to high temperature and CO2 conditions? -Lower ambient DNA methylation may be related to increased resistance to stress -DNA methylation plays a role in coral phenotypic plasticity -Different coral species have different ambient levels of DNA methylation -Phenotypic plasticity varies between coral species
A
Which of the following is true about phenotypic plasticity? -A certain genotype may be able to produce a range of phenotypic responses to different environmental conditions -Phenotypic plasticity refers to the ability of an organism to maintain a constant response even in changing environmental conditions -A certain genotype is only able to produce a single phenotype -Phenotypic plasticity is a slow process and only occurs after many generations of natural selection
A
Which of the following is true regarding transgenerational inheritance of environmental memory in corals? A.All answers are correct. B.DNA methylation patterns related to stress tolerance can be transmitted between parent corals and larvae C.Larvae from parent corals that were exposed to temperature and CO2 stress demonstrated higher stress tolerance than larvae from parents that were maintained at ambient conditions D.Transgenerational inheritance of environmental memory would greatly increase the benefit of coral preconditioning treatments in coral restoration
A
Which of the following is true... -Genetic imprinting is Cis-acting -Genetic imprinting only occurs after birth -Genetic imprintings is Trans-acting -Genetic imprinting occurs on both chromosomes
A
Which of the following scenarios provides evidence of environmentally-induced transgenerational epigenetic inheritance? a)We find epigenetic marks indicative of exposure to metal contaminants in the eggs of sea urchins, although only their grandparents experienced the metal exposure. b)We find certain epigenetic marks in sea urchins experiencing 25℃ water. When their offspring (F1) are exposed to 25℃, we find these same epigenetic marks in their sperm. c)We find that the scent of acetophenone led to the incorporation of certain epigenetic marks in a mouse's olfactory epithelium, and these same marks are present in the mouse's sperm cells. d)We find lower levels of DNA methylation in genes encoding heat shock proteins in the liver cells of a mouse exposed to high temperature stress.
A
Why does imprinting need to happen before fertilization -So the new cell knows which genome is paternal and which maternal. -In order to facilitate dosage compensation -Because without imprinting, fertilization is not possible -none of the answers are correct.
A
Explain, in no more than 2 sentences, what is the most common function for imprinted genes.
Although there is no specific common function, imprinted genes are usually involved in embryonic/neonatal regulation. Maternally expressed genes are usually involved in repressing offspring growth, while paternally expressed genes are involved in the opposite.
Because most cancers are multifactorial, the most effective therapies: -Require epigenetic therapies -Use combinatorial therapies of multiple drugs often along with chemotherapy -Use only chemotherapy because most drugs create resistance eventually -Use a single drug at a time and chemotherapy
B
Histone Phosphorylation plays a role in : -Cell division -All answers are correct -Apoptosis -DNA damage repair
B
In the younger stages of an embryo, how are the cellular functions directed/regulated? -The embryo creates its own TFs, and proteins to direct processes -Through epigenetic markers present in the embryo remaining from the parental gametes -Due to proteins transferred through sperm in fertilization -Through influences of diet and environmental stressors or interactions
B
In which order does the list of cell types go from the most potent to least potent (ability to become all types of cells to ability to become few cell/tissue types)? -Totipotent; multipotent; pluripotent -Totipotent; pluripotent; multipotent -Multipotent; pluripotent; totipotent -Pluripotent; multipotent; totipotent
B
The erasure of repressive epigenetic marks in primordial germ cells... -Leads to a somatic fate -Leads to totipotency -All answers are correct -Involves a very limited epigenetic reprogramming
B
The first imprinted genes were discovered in ... -the early 1970s -the early 1990s -the early 2000s -the early 1980s
B
The inactive X chromosome is characterized by the presence of _________ and it is also called _________. -Euchromatin, Barr body -Heterochromatin, Barr body -Heterochromatin, Xist -Euchromatin, Xist
B
What conclusion can be drawn from the purple sea urchin study regarding transgenerational plasticity?(This Question the answer is unclear because he gave credit to everybody... I don't remember what he ended up saying was the right answer) ( He says it's B on the discussion board) A.Embryos with many highly methylated genes tended to be larger in body size B.Differences in epigenetic marks, gene expression, and phenotype can persist in offspring as a result of the parental generation's environment, regardless of the environmental conditions the offspring generation experiences C.Environmental conditioning altered histone acetylation in the adults, and mothers passed on these epigenetic marks to their offspring D.Paternal effects cannot contribute to transgenerational plasticity because unlike mothers that can alter how resources are provisioned to their eggs (e.g., lipids), fathers cannot alter how resources are provisioned to their sperm
B
What was the outcome of the study that examined acetophenone exposure in mice? -Parents socially transmitted the fear of acetophenone by communicating their environmental experience to their offspring -Exposure to acetophenone paired with an electric shock influenced the neural structure and behavior of subsequent generations naïve to the electric shock -Transgenerational epigenetic inheritance occurred in natural populations of the mice -Only mice that personally experienced the acetophenone scent paired with an electric shock developed enhanced olfactory senses and a fear behavior
B
Which of the following is true... -Genetic imprinting only occurs after birth. -Genetic imprinting is Cis-acting. -Genetic imprinting occurs on both chromosomes. -Genetic imprinting is Trans-acting.
B
Which of the following statements about transgenerational plasticity is true? -An organism's phenotype is more likely to be affected by its own environment than by its parent's environment. -An organism's phenotype can be affected by the environment experienced by its grandparents. -The mother's environment cannot influence offspring phenotype. -The father's environment cannot influence offspring phenotype.
B
Which of the following statements are true? A.Epigenetic marks can only facilitate an organism's response to environmental stress if it is incorporated into its germline. B.Transgenerational plasticity could be maladaptive if conditions change such that parents and their offspring experience very different environments. C.The environment changes an organism's epigenome by directly altering its phenotype. D.Transgenerational epigenetic inheritance cannot influence evolutionary processes because it is non-genetic.
B
_____ Residues are methylated by ______ -Arginine, Hats -Lysine, KMTS -erine, DNMTS -Lysine, HATS
B
Chronic ethanol treatment: -Is associated with gene expression -Its effects on chromatin state has not being elucidated -Is associated with chromatin repression and gene silencing due to hyper methylation upon withdrawal from treatment -Is associated with neuroadaptation and therefore withdrawal from it is associated with gene up-regulation
C
How can environmental epigenetics be applied to coral conservation? -Epigenetic modifications related with stress tolerance may be transmitted across generations, increasing the chance for long-term benefits -Preconditioning corals to stress may increase coral stress tolerance and therefore survival -All answers are correct. -Phenotypic plasticity and epigenetic memory may allow corals to rapidly adapt to the changing climate
C
In Humans which process regulates germ-cell specification? -Waddington Landscape processes -Transgenerational epigenetic inheritance -Epigenesis (pluripotent cells acquire germ cell fate in response to inductive signals) -Preformation (maternal inheritance of preformed germ cells)
C
In which order does the list of cell types go from the most potent to least potent (ability to become all types of cells to ability to become fe cell/tissue types)? -Totipotent, multipotent, pluripotent -Multipotent, pluripotent, totipotent -Totipotent, pluripotent, multipotent -Pluripotent, multipotent totipotent
C
Pluripotent cells can do which of the following? -Create any cell type and a new individual -Create only specific tissue types -Each cell can create any type of cell but not an individual -Create specific organ system
C
The erasure of repressive epigenetic marks in primordial germ cells ... -Leads to a somatic fate -Involves a very limited epigenetic reprogramming -Leads to totipotency -All answers are correct
C
The first imprinted genes were discovered in ... -the early 2000s -the early 1980s -the early 1990s -the early 1970s
C
Totipotent cells can do which of the following? -Create specific organ systems -Create only certain tissue types -Create any type of cell and a new individual -Differentiate into only germinal cells
C
What conclusion can be drawn from the purple sea urchin study regarding transgenerational plasticity? -Paternal effects cannot contribute to transgenerational plasticity because unlike mothers that can alter how resources are provisioned to their eggs (e.g., lipids), fathers cannot alter how resources are provisioned to their sperm -Embryos with many highly methylated genes tended to be larger in body size -Differences in epigenetic marks, gene expression, and phenotype can persist in offspring as a result of the parental generation's environment, regardless of the environmental conditions the offspring generation experiences -Environmental conditioning altered histone acetylation in the adults, and mothers passed on these epigenetic marks to their offspring
C
Where will epigenetic marks be less stable -in all of them. -Pluripotent cells -Totipotent cells -Multipotent cells
C
Which of the following is an example of a context-dependent epigenetic effect? A. A histone variant located at a given genomic region is acetylated after the F0 generation experienced a severe drought, and this same histone is found to be acetylated at the same genome region in the F2 generation's germline despite the disappearance of drought conditions B.A specific gene is demethylated after the F0 generation experienced a severe drought, and the gene is found to be demethylated in the F2 generation's germline despite the disappearance of drought conditions C.A histone variant that is present in the F0 generation during temperatures stress is only present in the F1 generation when it too experiences temperature stress D.None of the answers is correct
C
Which tissue/cell type in an embryo gives rise to the cells belonging to the germ line -TE (Trophoectoderm) -Mesodermal cells -PCGs (Primordial Germ Cells) -ICM (Inner Cell Mass)
C
CpG islands in cancer cells: -Methylation patterns have not been identified in CpG islands -Tend to be hypo-methylated compared to normal cells -Have distinctive repressive marks and no activating marks. -Usually are hyper-methylated and bivalent
D
How is it generally defined the combinatorial influence that one or more histone PTMs have on the deposition , interpretation or erasure of other histone modifications? -Lysine crosstalk -Histone crossing over -Gene crosstalk -Histone crosstalk
D
Mary Lyon was responsible for discovering ... -The X chromosome in females -The sex chromatin body -All answers are correct. -That the Barr body constitutes an inactive X chromosome
D
Multipotent cells can do which of the following? -Only create specific organ systems -Only create one cell type -Create any cell type and a new individual -Differentiate and form a variety of tissue types
D
Preformation involves ... -None of the answers is correct -Acquisition of germ cell fate in response to inductive signals -Acquisition of somatic cell fate in response to inductive signals -Maternal inheritance of preformed germ cells
D
The Sry gene is also known as: A. The X-chromosome silencing gene B. The dosage regulation gene C. The sex-determining or female gene D.The sex determining or male gene
D
What is the only way in which differentiated cells can return to the top of Waddington's landscape -By undergoing DNA demethylation -By undergoing crossing-over -They cannot. -By producing germ cells that will form an undifferentiated zygote
D
Which of the following is not a predicted result for the project involving nursery corals on Bonaire? A.Coral epigenetic responses are expected to vary with environmental conditions such as different water temperatures and nutrient concentrations. B.Differences are expected between the epigenomes of coral clones (same genotype) that have been living at different sites. C.Corals native to the "high stress" site are predicted to have acquired a higher stress tolerance compare to corals native to the "low stress" site. D.Coral genotype is the only factor that is predicted to influence coral performance and stress tolerance.
D
Which of the following is required for epigenetic memory? -The environment must remain constant with no deviations from ambient conditions -A second stress exposure must elicit a similar or worse (more detrimental) stress response -Epigenetic modifications must be reset after a return to normal conditions -Epigenetic modifications must be maintained after a return to normal conditions
D
In general, the concept of dosage compensation describes: -A process in which both X chromosomes of a female organism under-express all of their genes. -A process that is unique to humans in which the level of expression of genes found in the X-chromosome is equalized in males and females. -A process in which some genes are overexpressed in mammal males to overcome the fact that they only possess one X chromosome. -A process observed in several sexually reproducing organisms in which the level of expression of genes found in sex chromosomes is equalized in males and females.
D -A process observed in several sexually reproducing organisms in which the level of expression of genes found in sex chromosomes is equalized in males and females.
Epigenetic Modifications like chromatin remodeling complexes and histone mutation are not among the key components of cancer -True -False
False
Provide 2 examples of epigenetic alterations that have been linked to cancer
Global DNA hypomethylation is usually associated with malignant cells; Mutation of histone methyltransferase (KMTs) is also linked to cancer.
In your own words, describe how epigenetic memory can increase stress tolerance.
If epigenetic modifications acquired during a stress event are maintained, these modifications may prepare the organism to respond more quickly to a subsequent stress exposure, therefore resulting in a less detrimental effect on the organism
Explain, in no more than 3 sentences, why is dosage compensation required and how is it achieved in mammals.
It is required due to the presence of chromosomal sex determination. It is achieved by the inactivation of one chromosome in the homogametic sex (eg, XX). Inactivation involves epigenetic mechanisms including histone PTMs and variants, DNA methylation and small RNAs).
Explain in 2 sentences the major mechanisms regulating germ cell specification
Performation, consisting of the maternal inheritance of preformed germ cells, such as in the case of drosophila. Epigenesis, where pluripotent cells acquire germ cell fate in response to inductive signals.
Let's say we find that temperature stress causes rabbits to rapidly lighten their coat color via increased DNA methylation of a specific pigment gene. We find this epigenetic mark (increased methylation of the pigment gene) in their sperm. How could we investigate the potential for transgenerational epigenetic inheritance in these rabbits?
See if their offspring exhibit the lightened coat phenotype and the increased methylation of the pigment gene without being exposed to temperature stress or interacting with the F0 generation.
Define the term Bivalent histone domain:
These are histone modifications that coexist in the same chromatin region and are associated with activation and repression, changing and complex landscaped that evolves in a cell context-dependent fashion.
Explain, in a SINGLE sentence, how is it possible that many X-linked genes escape inactivation in mammals.
They escape inactivation because they are mostly located in PAR (pseudo-autosomal regions) regions, where X and Y chromosomes have homologous regions.
Non-Coding RNAs have been associated with cancer: -True -Flase
True
