Ch 17
epigenetics
DNA methylation, chromatin remodeling, covalent histone modification and localization of histone variants are all examples of ________.
tissue-specific
Genes that are highly regulated and may be expressed only in certain cell types are called __________-___________ genes.
pheomelanin is not produced.
Mice that are homozygous for the loss-of-function mutation in the Agouti gene will have black fur because the mice are albino. melanin is not produced. pheomelanin is not produced.
Epigenetic changes are transmissible from cell to cell. Epigenetic changes may be transmitted to offspring. Variations of gene expression are unrelated to variations in the DNA base sequence. Variations are reversible from one generation to the next.
Select all of these that are true regarding epigenetics. Epigenetic changes are transmissible from cell to cell. Epigenetic changes may be transmitted to offspring. Variations of gene expression are unrelated to variations in the DNA base sequence. Variations are reversible from one generation to the next. Variations of gene expression result from mutations.
imprinting control differentially methylated
The Igf2 gene in mammals is only expressed from the paternal chromosome. This is due to different patterns of DNA methylation during oogenesis and spermatogenesis. Methylation can occur at two different sites: the ___________ _________ region (ICR), and the _____________ _________region (DMR).
iron response element (IRE)
The region of the ferritin and the transferrin receptor mRNAs that the iron-regulatory protein (IRP) binds to is called the __________ __________ ________
imprinting control differentially methylated
This figure shows the region of a chromosome that contains the Igf2 and H19 genes in mammals. ICR refers to __________ ________ region, while DMR stands for __________ ______region.
Tsix, Xist
Transcription factors called pluripotency factors stimulate the expression of ______, which inhibits the expression of ______ to keep both X chromosomes in an active state during early embryogenesis. Xist, Tsix Igf2, Fgl2 Igf2, Xist Tsix, Xist
True The IRP exerts its effects by binding to the iron response element, which is found in the mRNAs the encode both ferritin and the transferrin receptor.
True or false: The iron-regulatory protein (IRP) binds to a regulatory sequence in mRNA called the iron response element (IRE). True False
Both activation and repression.
What effect can ATP-dependent chromatin remodeling have on transcription? Repression only. Both activation and repression. Activation only.
150 bp
What is the size of the nucleosome-free region found at the core promoter of active genes? 15 bp 150 bp 15,000 bp 1,500 bp
f. all of the above can have an epigenetic effect on gene expression
which of the following are examples of molecular changes that can have an epigenetic effect on gene expression? a. chromatin remodeling b. covalent histone modification c. localization of histone variants d. DNA methylation e. feedback loops f. all of the above can have an epigenetic effect on gene expression
In part (a), DNA methylation blocks an activator protein from binding to the DNA. This prevents transcriptional activation
Explain why the events shown in part (a) inhibit transcription.
transcription factor
A _____________ __________is a protein that influences the ability of RNA polymerase to transcribe a given gene.
b. 5'-TGAC-3' 3'-ACTG-5'
A bidirectional enhancer has the following sequence: 5'-GTCA-3' 3'-CAGT-5' Which of the following sequences would also be an enhancer? a. 5'-ACTG-3' 3'-TGAC-5' b. 5'-TGAC-3' 3'-ACTG-5' c. 5'-GTCA-3' 3'-CAGT-5' d. 5'-TGAC-3' 3'-ACTG-5'
nucleosomes
A change in chromatin confirmation from closed to open often involves the movement of genes. promoters. helicases. nucleosomes.
Brown with black tips
Adult, wild-type mice with genotype AA for the Agouti gene will have what color coat hairs? All brown Yellow with brown tips Brown with black tips All black All yellow
a. true example: activator proteins (a type of regulatory transcription factor protein) bind to enhancers. Repressors are the opposite, they bind to regulatory sequences called silencers to down regulate. b. False general transcription factors bind to it not regulatory transcription factors c. true d. false The binding of a Transcription factor to an enhancer causes upregulation from 10x to 1000x
Are the following statements true or false? a.An enhancer is a type of regulatory element b.A core promoter is a type of regulatory element c.Regulatory transcription factors bind to regulatory elements d.An enhancer may cause the down regulation of transcription
DNA methylation
As a result of a diet of royal jelly, queen bees develop differences in _____ when compared with worker bees. DNA methylation nucleosome placement histone methylation histone phosphorylation histone acetylation
Gene regulation is most energy-efficient at the level of transcription, because a cell avoids wasting energy making RNA or Proteins.
At which of these levels is regulation of gene expression most energy-efficient? transcription RNA processing translation posttranslational modifications
ATP-dependent chromatin remodeling complexes may change the positions of nucleosomes, evict histones, and/or replace histone with histone variants.
Briefly describe three ways that ATP-dependent chromatin-remodeling complexes may change chromatin structure.
b. the combination of several factors determines the expression of any given gene
Combinatorial control refers to the phenomenon that a. transcription factors always combine with each other when regulating genes b. the combination of several factors determines the expression of any given gene c. small effector molecules and regulatory transcription factors are found in many different combinations d. genes and regulatory transcription factors must combine with each other during gene regulation
yellow fur.
Mice with a gain-of-function mutation in the Agouti gene will have black fur. yellow fur. brown fur. white fur.
Histone modifications may directly affect the interaction between histones and the DNA, or they may affect the binding of other proteins to the chromatin.
Describe two different ways that histone modifications may alter chromatin structure
Regulatory elements are relatively short genetic sequences that are recognized by regulatory transcription factors. After the regulatory transcription factor has bound to the regulatory element, it will affect the rate of transcription, either increasing or decreasing it, depending on the action of the regulatory protein. Regulatory elements are typically located in the upstream region near the promoter, but they can be located almost anywher (i.e., upstream and downstream) and even quite far from the promoter.
Discuss the structure and function of regulatory elements. Where are they located relative to the core promoter?
activation repression
During Drosophila development, the protein complex trithorax group (TrxG) causes gene ___________, while polycomb group (PcG) complex causes gene ___________.
TrxG PcG
During development in Drosophila, the protein complex _________ causes gene activation, while _______ complex causes gene repression.
epigenetic
During embryonic development, many genes undergo _________ changes that enable them to be transcribed or cause them to be permanently repressed.
Histone eviction or displacement is needed for elongation to occur because RNA polymerase cannot transcribe through nucleosomes. It needs to unwind the DNA for transcription to take place.
Explain why histone eviction or displacement is needed for the elongation phase of transcription to occur
ferritin
Excess iron in animal cells is stored within a hollow, spherical protein known as ________.
During oogenesis, the ICR and DMR are not methylated. This allows CTCF to bind to these sites and to each other to form a loop. This loop prevents a nearby enhancer from activating the Igf2 gene. During sperm formation, methylation of these sites prevents CTCF binding and thereby prevents loop formation. The nearby enhancer activates the Igf2 gene. Therefore, the copy of the Igf2 gene inherited from the father via sperm is active.
Explain how DNA methylation and the formation of a DNA loop control the expression of the Igf2 gene in mammals. How is this gene imprinted so that only the paternal copy is expressed in offspring?
queen bees.
Female honeybee larvae fed royal jelly during development will become queen bees. worker bees.
worker bees.
Female honeybee larvae fed royal jelly during early development, and nectar or pollen later in development will become worker bees. queen bees.
During embryogenesis, the X chromosomes pair up and a symmetry break causes the pluripotency factors to move to one X chromosome, which remains active. The other X chromosome expresses the Xist gene. The Xist RNA binds to XIC and then spreads to both ends of the X chromosome. The Xist RNA recruits proteins to this X chromosome that cause it to become more compact and be inactive with regard to the expression of most genes. Xist is not silenced
Following X-chromosome inactivation, most of the genes on the inactivated X chromosome are silenced. Explain how. Name one gene that is not silenced.
Methylation results in proteins binding to the methylated cytosine and inhibiting transcription
How does methylation affect transcription?
In a low iron cellular environment, iron regulatory protein (IRP) binds to the iron response element (IRE) and inhibits translation of ferritin protein. In a high iron environment IRP binds to and is inactivated by iron ions. Translation of ferritin protein is then free to proceed.
How is translation affected by low iron? High iron?
transferrin
In animals, the major protein that carries iron in the bloodstream is transferrin. ferritin. calmodulin. hemoglobin.
the deposition of yellow pigment in hair.
In mice, the Agouti gene regulates the sex of mice. the transcription of cell cycling proteins. the deposition of yellow pigment in hair. the size of mice.
barr
In somatic cells of female mammals, one of the two X chromosomes becomes a condensed _________ body, where the genes are inactivated
iron-regulatory proteins which can bind to mRNA.
Iron assimilation in mammalian cells is regulated by iron-regulatory proteins which can bind to mRNA. transient methylation of the ferritin and transferrin genes. histone modification of the ferritin and transferrin genes. RNA silencing of genes involved in iron transport.
acetyltransferases
Lysine residues on core histone proteins can be acetylated by enzymes called histone ____________.
black fur
Mice that are homozygous for the loss-of-function mutation in the Agouti gene will have brown fur white fur yellow fur black fur
H2A.Z H2A
Nucleosomes containing the histone variant ___________, which are usually found at the +1 nucleosome, are thought to be more easily removed from the DNA than those containing the standard histone ____________.
pluripotency
Prior to X-chromosome inactivation, ____________ factors stimulate the expression of Tsix to maintain the activity of both X chromosomes.
royal methylation
Queen bees differ from worker bees because they have been fed ________ jelly throughout their lifespan and show differences in DNA ___________ that affect expression of many of their genes.
regulation
The phenomenon where gene expression is controlled so that genes can be expressed at high or low levels is called gene ________
nucleosomes
The placement of at ________ or near promoters often plays a key role in whether a gene is active or inactive.
receptor
The regulatory transcription factors that respond to glucocorticoid hormones are called glucocorticoid __________
x inactivation
The two genes Xist and Tsix play a role in _______- chromosome __________.
iron-regulatory
The two mRNAs that encode ferritin and the transferrin receptor are both influenced by an RNA-binding protein known as the ________-________ protein.
Xist and Tsix
Two genes that play a role in X-chromosome inactivation are XCI and ICX ferritin and transferrin receptor Igf2 and Fgl2 Xist and Tsix
Regarding honeybees and agouti mice, specific dietary consumption was correlated with changes in DNA methylation.
Using coat color and the development of female honeybees as examples, explain how dietary factors cause epigenetic modifications and thereby lead to phenotypic effects.
a nucleosome-free region (NFR) is found at the beginning and end of many genes. Nucleosomes tend to be precisely positioned near the beginning and end of a gene, but are less regularly distributed elsewhere. in active genes they're located around the core promoter and are about 150 bp long.
What is a nucleosome-free region? Where are they typically found in a genome? How are nucleosome-free regions thought to be functionally important?
de novo methylation
What is the process called in which completely unmethylated DNA becomes methylated?
epigenetic changes
What type of mechanism is responsible for enabling the transcription of muscle-specific genes in an embryonic cell that will eventually give rise to muscle tissue? epigenetic changes mutations of the DNA sequences post-translational modification of proteins
methylated hemimethylated
When a fully methylated DNA segment of DNA is replicated, the newly made daughter strand contains _________ cytosines. This DNA is said to be _______.
the gene is over-expressed, resulting in yellow fur.
When there is a gain-of-function mutation in the mouse Agouti gene the gene is expressed normally, resulting in wild-type brown fur with black tips. the gene is not expressed, resulting in white fur. the gene is over-expressed, resulting in yellow fur. the gene is over-expressed, resulting in black fur.
somatic cells of female mammals.
X-chromosome inactivation occurs in gamete-producing cells of female mammals. somatic cells of male mammals. somatic cells of both male and female mammals. somatic cells of female mammals. gamete-producing cells of male mammals.
c. both a and b
an epigenetic modification to a specific gene may initially be established by a. a transcription factor b. a non-coding RNA c. both a and b d. none of the above
d. be both a and b
epigenetic changes may a. be programed during development b. be caused by environmental changes c. involve changes in the DNA sequence of a gene d. be both a and b
a. inhibition of translation of the ferritin mRNA
the binding of iron regulatory protein (IRP) to the iron response element (IRE) in the 5'-untranslated region of the ferritin mRNA results in a. inhibition of translation of the ferritin mRNA b. stimulation of translation of the ferritin mRNA c. degradation of the ferritin mRNA d. both a and c
b. de novo methylation.
the process in which completely unmethylated DNA becomes methylated is called a. maintenance methylation b. de novo methylation. c. primary methylation d. demethylation.
histone
Core ___________ proteins contain a globular domain and a flexible amino-terminal tail. DNA wraps around the globular domains, and the amino-terminal tails protrude from the chromatin.
housekeeping genes.
Genes that code for proteins that are required in most cells of a multicellular organism are called CpG islands. housekeeping genes. tissue-specific genes. promoter genes.
The attachement of acetyl group (-COCH_3) eliminates the positive charge on the lysine side chain, thereby disrupting the electrostatic attraction between the histone protein and the negatively charged DNA backbone. This makes it easier for the histones to be displaced from the DNA.
How does histone acetyltransferase affect nucleosome structure and transcription?
the attraction between DNA and histones occurs because the histones are positively charged and the DNA is negatively charged. The covalent attachment of acetyl groups decreases the amount of positive charge on the histone proteins and thereby may decrease the binding of the DNA. In addition, histone acetylation may attract proteins to the region that loosen chromatin compaction.
explain how the acetylation of core histones may loosen chromatin packing
coactivator
A protein that increases the rate of transcription but does not directly bind to the DNA is called a __________
activator
A regulatory transcription factor that enhances the rate of transcription is called a(n) __________
This person would be unable to make ferritin, because the IRP would always be bound to the IRE. The amount of transferrin receptor mRNA would be high, even in the presence of high amounts of iron, because the IRP would remain bound to the IRE, stabilizing the transferrin receptor mRNA. Such a person would not have any problem taking up iron into his or her cells and, in fact, would take up a lot of iron via the transferrin receptor, even when the iron concentrations were high. Therefore this person would not need more iron in the diet. However, excess iron in the diet would be very toxic for two reasons. First the person cannot make ferritin, which prevents the toxic build up or iron in the cytosol. Second, when iron levels are high, the person would continue to synthesize the transferrin receptor, which functions in the uptake of iron.
Suppose that a person is homozygous for a mutation in the IRP gene that changed the structure of the IRP in such a way that it could not bind iron, but it could still bind to IREs. How would this mutation affect the regulation of ferritin and transferrin receptor mRNAs? Do you think such a person would need more iron in his or her diet than normal individuals? Do you think that excess iron in the diet would be more toxic than it would be for normal individuals?
True DNA methylation patterns are retained following DNA replication and into future daughter cells.
True or false: The methylation state of DNA is inherited during cell division. True False
Dietary factors can affect the occurence of epigenetic changes, particularly those that happen during early stages of development. For example, dietary factors that affect the level of DNA methylation appear to be responsible or partly responsible for altering coat color in mice and affecting female bee development. These dietary factors may affect the level of S-adenosylmethionine and/or the function of DNA methyltransferase and thereby influence whether particular genes are methylated or not. If genes are methylated, this typically inactivates them.
Using coat color in mice and the development of female honeybees as examples, explain how dietary factors cause epigenetic modifications and thereby lead to phenotypic effects.
Histone acetyltransferases
What enzymes can add acetyl groups onto the lysines of core histone proteins? Histone lysinases Histone acetylases Histone deacetylases Histone acetyltransferases
For the glucocorticoid receptor to bind to a GRE, a steroid hormone must first enter the cell. The hormone then binds to the glucocorticoid receptor, which releases HSP90. The release of HSP90 exposes a nuclear localization signal (NLS) within the receptor, which enables it to dimerize and then enter the nucleus. Once inside the nucleus, the dimer binds to a GRE, which activates transcription of the adjacent genes.
describe the steps that need to occur for the glucocorticoid receptor to bind to a GRE
epigenetic
Variation of gene expression that is transmissible and reversible but not related to the variation in the DNA is called ___________
When an activator interacts with mediator, it causes mediator to phosphorylate CTD, which causes RNA polymerase to proceed to the elongation phase of transcription.
when an activator protein interacts with mediator, how does this affect the function of RNA polymerase?
Transcriptional activation occurs when a regulatory transcription factor binds to a regulatory element and activates transcription. These transcriptional activator proteins may interact with TFIID and/or mediator to promote the assembly of RNA polymerase and general transcription factors at the promoter region. They may also alter the structure of chromatin so that RNA polymerase and transcription factors are able to gain access to the promoter. transcriptional inhibition occurs when a regulatory transcription factor inhibits transcription. Such repressors may interact with TFIID and/or mediator to inhibit RNA polymerase.
What are the functions of transcriptional activator proteins and repressor proteins? Explain how they work at the molecular level.
Recruit proteins that affect nucleosomes Influence the function of TFIID Influence the function of mediator
What are the most common ways that regulatory transcription factors influence the ability of RNA polymerase II to transcribe a given gene? Deletion of the TATA box Recruit proteins that affect nucleosomes Influence the function of TFIID Influence the function of mediator Bind directly to RNA polymerase II
A nucleosome-free region (NFR) is a location on a chromosome where nucleosomes are missing. These regions are typically found at the beginnings and ends of genes. An NFR at the beginning of a gene is thought to be important for activation of the gene. An NFR at the end of a gene may be important for its proper termination.
What is a nucleosome-free region? Where are such regions typically found in a genome? How are nucleosome-free regions thought to be functionally important?
a. a greater level of DNA methylation and a decrease in the expression of Agouti gene
When mice carrying the A^vy allele exhibit a darker coat, this phenotype is thought to be caused by dietary factors that result in a. a greater level of DNA methylation and a decrease in the expression of Agouti gene b. a lower level of DNA methylation and a decrease in the expression of the Agouti gene. c. A greater level of DNA methylation and the overexpression of the Agouti gene. d. a lower level of DNA methylation and the over expression of the agouti gene
The agent in cigarette smoke may have caused the methylation of CpG islands near the promoter of the p53 gene, thereby inhibiting transcription. Another possibility is that it may affect covalent histone modifications or chromatin remodeling in a way that causes the gene to be in a closed conformation.
A research study indicated that an agent in cigarette smoke caused the silencing of a tumor suppressor gene called p53. However, upon sequencing, no mutation was found in the DNA sequence for this gene. Give two possible explanations for these results.
nucleosome region
The core promoter of active genes is found in a(n) -free , which is a segment of DNA that is missing histones.
H2B H3 H1 H2A
Select the histones for which variants have been identified. H2B H3 H1 H4 H2A
Phosphorylation Acetylation Methylation
Select the common types of covalent modifications made to the amino-terminal tails of histones. Phosphorylation Ubiquitination Acetylation Methylation
d. Xist is expressed only on Xi, and Tsix is expressed only on Xi
for XCI to occur, where are the Xist and Tsix genes expressed? a. Xist is expressed only Xa, and Tsix is expressed only on Xi b. Xist is expressed only on XI, and Tsix is expressed only on Xa c. Xist is expressed only on Xa, and Tsix is expressed only on Xa d. Xist is expressed only on Xi, and Tsix is expressed only on Xi
By changing the histone modification patterns that are recognized by other proteins By influencing interactions between DNA and histones within nucleosomes
Select ways in which histone modifications affect the level of transcription. By moving histones out of the nucleus By stopping all transcription in the cell By changing the histone modification patterns that are recognized by other proteins By influencing interactions between DNA and histones within nucleosomes
Eventually, the glucocorticoid hormone will be degraded by the cell. The glucocorticoid receptor binds the hormone with a certain affinity. The binding is a reversible process. Once the concentration of the hormone falls below the affinity of the hormone for the receptor, the receptor will no longer have the glucocorticoid hormone bound to it. When the hormone is released, the glucocorticoid receptor will change its conformation, and it will no longer bind to the DNA.
The glucocorticoid receptor is an example of a transcriptional activator that binds to response elements and activates transcription. How could the function of the glucocorticoid receptor be shut off? (note: the answer to this question is not directly described in this chapter.)
up regulation.
An enhancer is a DNA element that is bound by a regulatory transcription factor, which leads to transcriptional repression. up regulation. DNA replication. down regulation.
At the level of DNA sequences, queen and worker bees are not different from each other. However, differences in gene expression due to epigenetics can explain the morphological differences between the two types of female bees.
Are queen and worker bees genetically different from each other?
1. Binding of an activator to an enhancer in the NFR 2. Recruitment of a chromatin-remodeling complex and a histone-modifying enzyme 3. Recruitment of general transcription factors and RNA Pol II to the core promoter, allowing the formation of a preinitiation complex 4. Eviction or destabilization of histone octamers, allowing RNA pol II to pass, and elongation to occur.
Place these steps in a simplified model for transcriptional activation of a eukaryotic gene in order from first to last. Binding of an activator to an enhancer in the NFR Recruitment of general transcription factors and RNA Pol II to the core promoter, allowing the formation of a preinitiation complex Eviction or destabilization of histone octamers, allowing RNA pol II to pass, and elongation to occur. Recruitment of a chromatin-remodeling complex and a histone-modifying enzyme Recruitment of general transcription
Perhaps the DNA methyltransferase is responsible for methylating and inhibiting a gene that causes a cell to become a muscle cell. The methyltransferase is inactivated by the mutation.
Let's suppose that a vertebrate organism carries a mutation that causes some cells that normally differentiate into nerve cells to differentiate into muscle cells. A molecular analysis reveals that this mutation is in a gene that encodes a DNA methyltransferase. Explain how an alteration in a DNA methyltransferase could produce this phenotype.
c. De novo methylation occurs in sperm, and maintenance methylation occurs in somatic cells of offspring.
For the Igf2 gene, where do de novo methylation and maintenance methylation occur? a. De novo methylation occurs in sperm, and maintenance methylation occurs in egg cells b De novo methylation occurs in egg cells, and maintenance methylation occurs in sperm cells. c. De novo methylation occurs in sperm, and maintenance methylation occurs in somatic cells of offspring. d. De novo methylation occurs in egg cells, and maintenance methylation occurs in somatic cells of offspring.
gene expression can be controlled so that genes can be expressed at high or low levels.
Gene regulation means that gene expression can be controlled so that genes can be expressed at high or low levels. only certain genes are included in the genome of a species. gene expression is controlled so that all genes in a genome are expressed at the same level.
DNA methyltransferase.
5-methylcytosine is formed by cytosine methyltransferase. DNA methyltransferase. RNA methyltransferase.
dependent chromatin
ATP-___________ __________ remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes.
a. influences chromatin structure
According to the histone code hypothesis, the pattern of histone modifications acts like a language that a. influences chromatin structure b. promotes transcriptional termination c. inhibits the elongation of RNA polymerase d. does all of the above.
coactivators.
Activator proteins often increase transcription through an interaction with repressors. RNA. coactivators. RNA polymerase.
enhancers.
Activators bind to enhancers. repressors. RNA. silencers.
methylated.
CpG islands near the promoters of tissue-specific genes are often hemimethylated. unmethylated. methylated. phosphorylated.
covalent
DNA methylation is the _________ attachment of methyl groups to DNA.
5 cytosine
DNA methyltransferase is an enzyme that attaches a methyl group to the __________ position of the ___________ base
regulatory sequences. control elements. regulatory elements.
DNA sequences in eukaryotes that can be bound by regulatory transcription factors, which then affect the ability of RNA polymerase to transcribe a particular gene are called regulatory sequences. operator sequences. control elements. regulatory elements. core promoters.
regulatory control
DNA sequences that are analogous to the operator sites found near bacterial promoters are called __________ elements or ___________ elements.
Epigenetics is the study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible, but do not involve a change in the sequence of DNA. Not all epigenetic changes are passed from parent to offspring. For example, those that occur in somatic cells, such as lung cells, would not be passed to offspring.
Define epigenetics. Are all epigenetic changes passed from parent to offspring? Explain
the glucocorticoid receptor binds specifically next to genes that have an adjacent GRE.
Explain why the glucocorticoid receptor binds specifically next to the core promoter of certain genes, but not next to the core promoter of most genes.
nucleosomes histone
Histone modifications can affect transcription levels by directly influencing interactions within ________, and also by altering the _________ code.
d. all of the above are possible ways for methylation to affect transcription.
How can methylation affect transcription? a. it may prevent the binding of regulatory transcription factors b. it may enhance the binding of regulator transcription factors c. it may promote the binding of methyl-CpG-binding proteins, which inhibit transcription d. all of the above are possible ways for methylation to affect transcription.
Nucleosome eviction may allow certain proteins access to bind to particular sites in the DNA
How might nucleosome eviction affect transcription?
The mutation would cause the overproduction of ferritin, because ferritin synthesis would occur even if iron levels were low.
If a mutation prevented IRP from binding to the IRE in the ferritin mRNA, how would the mutation affect the regulation of ferritin synthesis? Do you think there would be too much or too little ferritin?
If TFIID cannot bind to the TATA box, RNA polymerase will not be recruited to the core promoter, and therefore transcription will not begin
If a repressor prevents TFIID from binding to the TATA box, why does this inhibit transcription
methylated nonmethylated
If fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be ___________ . If the same sequence of nonmethylated DNA is introduced into a cell, it will be ______________ in daughter cells.
The choice occurs only during embryonic development
In X-chromosome inactivation, when is the choice made as to which X chromosome is inactivated? Does this choice occur in embryonic cells, in adult somatic cells, or both?
in most cell types.
In a multicellular organism, housekeeping genes tend to be expressed in most cell types. only in certain cell types. only during embryonic development. in all cell types.
unmethylated methylated
In general ____________ CpG islands correlate with active genes, and _____________ CpG islands correlate with suppressed genes.
d. any of the above
Regulatory transcription factors can be modulated by a. the binding of small effector molecules b. protein-protein interactions c. covalent modifications d. any of the above
RNA polymerase II to progress to the elongation stage of transcription.
Mediator controls the ability of RNA polymerase II to begin the termination stage of transcription. RNA polymerase I to progress to the elongation stage of transcription. RNA polymerase I to begin the initiation stage of transcription. RNA polymerase II to progress to the elongation stage of transcription. RNA polymerase II to begin the initiation stage of transcription.
variants
Most histone genes encode standard histone proteins, but some have accumulated mutations that change the amino acid sequence of the histone proteins. These proteins are called histone_________ .
receptor
Once inside the cell, the glucocorticoid hormone binds to a glucocorticoid _______, releasing it from a protein known as HSP90. receptor repressor response element enhancer activator
The choice of which X chromosome remains active occurs when the pluripotency factors and CTCFs, which were previously bound to both X chromosomes, shift entirely to one of the X chromosomes. Because the pluripotency factors stimulate the expression of the Tsix gene, the X chromosome to which they shift is chosen as the active X chromosome. By comparison, on the other X chromosome, the Tsix gene is not expressed, which permits the expression of the Xist gene
Outline the molecular steps in the process of X-chromosome inactivation (XCI). Which step plays a key role in choosing which of the X chromosomes will remain active and which will be inactivated.
Covalent histone modification Chromatin remodeling Localization of histone variants DNA methylation
Select all of these that are examples of epigenetics. Covalent histone modification Chromatin remodeling Localization of histone variants DNA mutation DNA methylation DNA translocation
CpG islands.
Stretches of DNA of 1000-2000 bp in length containing a high number of CpG sites and found near gene promoters are called transcription factors. stop codons. CpG islands. start codons.
TATA promoter
TFIID binds to the _________ box and helps recruit RNA polymerase II to the core _____________.
enhancer up
The binding of a regulatory transcription factor to a(n) _________ can stimulate transcription 10- to 1000-fold, which is called ______________ regulation.
methylation
The covalent attachment of a -CH3 group to DNA is known as DNA glycosylation. phosphorylation. acetylation. carboxylation. methylation.
bind to the TATA box and recruit RNA polymerase II to the core promoter.
The function of TFIID is to prevent the binding of RNA polymerase II to the core promoter. bind to the core promoter and recruit RNA polymerase II to the TATA box. bind to an enhancer to increase transcription from the core promoter. bind to the TATA box and recruit RNA polymerase II to the core promoter.
under the appropriate environmental conditions. at the proper time. in the correct cell type.
The function of regulatory transcription factors must be modulated to ensure that genes are turned on under the appropriate environmental conditions. at the proper time. all the time. in growing cells only. in the correct cell type.
mediator
The protein complex that facilitates the interaction between RNA polymerase II and regulatory transcription factors is called ____________
regulating the binding of the transcriptional complex to the core promoter. controlling the switch from the initiation to the elongation stage of transcription.
Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by preventing DNA replication. regulating RNA processing. regulating the binding of the transcriptional complex to the core promoter. controlling the switch from the initiation to the elongation stage of transcription.
False Most regulatory transcription factors do not bind directly to RNA polymerase, but rather exert their effects through TFIID, mediator, or nucleosome structure.
True or false: Most regulatory transcription factors bind directly to RNA polymerase. True False
True Regulatory transcription factor function is modulated to ensure genes are turned on at the right time, in the correct cell type, and under appropriate environmental conditions.
True or false: The function of regulatory transcription factors is modulated. True False
maintenance methylation.
When fully methylated DNA is replicated, it is initially hemimethylated. The hemimethylated DNA is recognized by DNA methyltransferase, which makes it fully methylated. This process is called de novo methylation. maintenance methylation. replication methylation.
b. the core promoter is found in a nucleosome-free region
Which of the following characteristics is typical of a eukaryotic gene that can be transcribed? a. the core promoter is wrapped around a nucleosome b. the core promoter is found in a nucleosome-free region c. the terminator is wrapped around a nucleosome d. None of the above characteristics is typical of a eukaryotic gene.
b. the attachment of ubiquitin to histone proteins
Which of the following mechanisms may be involved when PRC1 complexes silence gene expression? a. the compaction of nucleosomes b. the attachment of ubiquitin to histone proteins c. the direct inhibition of transcription factors, such as TFIID d. any of the above may be involved in silencing of gene expression by PRC1 complexes.
An NFR is needed at the core promoter so that transcription factors can recognize enhancers and preinitiation complex can form.
Why is an NFR needed at the core promoter for transcription to occur?
d. do all of the above
a chromatin-remodeling complex may a. change the locations of nucleosomes. b. evict nucleosomes from DNA c. replace standard histones with histone variants d. do all of the above
a knot-like structure would prevent proteins such as TFIID and RNA polymerase from binding to the gene and would thereby inhibit transcription of the gene.
describe how the compaction of nucleosomes into a knot-like structure could silence gene expression
Epigenetic modifications lead to changes in gene expression that persist from early development to adulthood. These changes allow some genes to be expressed in certain cell types but not in others. The trithorax and polycomb group complexes are involved in causing such epigenetic changes.
in general, explain how epigenetic modifications are an important mechanism for developmental changes that lead to specialized body parts and cell types. How do the protein complexes called the trithorax and polycomb groups participate in this process?
d. all of the above
transcriptional activation of eukaryotic genes involves which of the following events a. changes in nucleosome locations b. changes in histone composition within nucleosomes c. histone modifications d. all of the above
De novo methylation occurs on unmethylated DNA, whereas maintenance methylation occurs on hemimethylated DNA.
what is the difference between de novo methylation and maintenance methylation?
