Lesson 11: Ch17&21 Control of Gene Expression in Eukaryotes, Epigenetics

Effects: Genomic imprinting

-Diffferent genes are imprinted in egg v. sperm cells -In embryo, 1 copy is expressed at a different level than the -Egg - genes that speed up growth are imprinted -Sperm - genes that slow growth are imprinted -A mutation is an imprinted gene will have different effects, depending on which parent transmitted it.

In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify the statements as true or false. True

-Enhancer sequences are composed of DNA base pairs. -Enhancer sequences can be located thousands of base pairs downstream from the transcription start site.

False

-Enhancer sequences can alter transcription levels in the absence of a bound protein. -Transcription factors bind to the entire enhancer sequence. -Transcription factors always decrease transcription level

Effects:

-Epigenetic Changes Associated with Cell Differentiation

GAL system in yeast

-GAL4 protein binds to DNA called Upstream Activation Sequence (UAS) to activate gene expression of genes involved in galactose metabolism -GAL80 protein binds to GAL4 to stop it from doing it's job -Galactose allows GAL3 protein to bind to GAL80 to stop it from stopping GAL4

Processes: How are histone modifications maintained during DNA REPLICATION?

-Histones are divided between the two DNA molecules -Perhaps marks on the original histones are used to help mark the "new" histones similarly?

Inactive X chromosome

-Jpx expression promotes Xist expression -Xist coats the chromosome

Which description applies to epigenetic gene regulation? -protein modifications such as addition of a functional group, or structural changes such as folding -a gene cluster controlled by a single promoter that transcribes to a single mRNA strand -processing of exons in mRNA that results in a single gene coding for multiple proteins -mRNA modifications such as additions of a 5′5′ cap and 3′3′ poly‑A tail and removal of introns -heritable changes in gene expression that occur without altering the DNA sequence

-heritable changes in gene expression that occur without altering the DNA sequence

4. No effect

A transcriptional activator binds an enhancer sequence.

Each answer box represents a mechanism by which eukaryotes can regulate gene expression. Determine which of the five mechanisms each example represents. Not all examples will be used. Changes in chromatin structure

Acetylation of histones facilitates transcription.

RNA processing

Alternative splicing produces different transcripts from the same gene.

dentify each description as typical of eukaryotic repressors or bacterial repressors. Leave unplaced the description that is not characteristic of either group. Eukaryotic repressor

Bins to a silencer that uses transcriptional activator proteins to block RNA polymerase

•Mechanisms of Gene Regulation by RNA interference

Interfering with the information passed from RNA to amino acid: −RNA cleavage −Inhibition of translation Inhibition of the actual transcription: −Transcriptional silencing: altering chromatin structure −Silencer-independent degradation of mRNA

Initiation of translation

Limited availability of initiation factors prevents translation of mRNA.

Match each term with its definition. a sequence of DNA located upstream of a gene that signals the start of transcription

Promoter

RNA interference

The RISC degrades mRNA complexed with miRNA or siRNA.

Processes: DNA methylation

The addition of methyl groups to nucleotide bases (often C) -often causes gene silencing -Can be maintained through DNA Replication.

What would be required to prove that a phenotype is caused by an epigenetic change? -The phenotype must be the result of a nucleotide change that is present in one gender but not the other. -The phenotype must be unexplained by known genetic mechanisms. -The phenotype must be passed to progeny only through the maternal DNA. -The phenotype must be reversible in the presence of mutagenic compounds. -The phenotype must be heritable with modified chromatin and an unaltered nucleotide sequence.

The phenotype must be heritable with modified chromatin and an unaltered nucleotide sequence.

Activity of transcription apparatus

Transcriptional activators increase promoter activity by interacting with the RNAPII holoenzyme.

-----CH21----- What is epigenetics?

Variation in a phenotype that is not caused by differences in the DNA sequence -Often caused by changes in chromatin, some of which are heritable. -from parent to progeny cells. -From parent to progeny organisms.

Which description is the best definition of a stem cell? a type of blood cell that does not have a nucleus, mitochondria, or other organelles a specialized cell that divides by meiosis to produce gametes in order to facilitate sexual reproduction a type of lymphocyte made in bone marrow that contributes an adaptive immune response an undifferentiated cell that can replicate itself indefinitely and differentiate into specialized cell types when appropriate

an undifferentiated cell that can replicate itself indefinitely and differentiate into specialized cell types when appropriate

Eukaryotic Cells features of Gene Regulation (different from Prokaryotic)

•Each structural gene has its own promoter, and is transcribed separately. •DNA must unwind from the histone proteins before transcription. •Transcription and translation are separated in time and space.

Translational regulation

•Proteins bind 5′ UTR •Affect availability of translational machinery

The Initiation of Transcription Is Regulated by Transcription Factors and Regulator Proteins

•Silencers •Sites where repressor proteins bind •Enhancers and Insulators •Enhancer: DNA sequence stimulating transcription from a distance away from promoter •Insulator: DNA sequence that blocks or insulates the effect of enhancers

•Coordinated gene regulation often performed via Response elements [instead of Operons]

•common regulatory elements upstream of the start sites of genes that are expressed in response to a common environmental stimulus

Histone modification

−Addition of methyl groups - Can either cause condensation or relaxation of chromatin, depending on location of methyl groups −Addition of acetyl groups to histone proteins −Typically causes relaxation of chromatin

•Gene regulation through RNA splicing

−Alternative splicing in Drosophila sexual development

DNA Methylation

−DNA methylation of cytosine bases adjacent to guanine nucleotides (CpG)-CpG islands −Represses transcription until removed

Histone modification:::•Acetylation of histones controls flowering in Arabidopsis

−Flowering locus C (FLC) gene - encodes a transcription factor that represses genes needed for flowering −Flowering locus D (FLD) gene - encodes a deacetylase that represses FLC, thereby de-repressing flowering

•Transcriptional Activators and Coactivators

−Stimulate and stabilize basal transcription apparatus at core promoter

Select the terms that represent a mode of regulation of gene expression in eukaryote -B‑form DNA structure -transcription -pyrimidine ring structure - posttranslational modification - mRNA splicing

transcription posttranslational modification mRNA splicing

21.3 Epigenetic Processes Produce a Diverse Set of effects

- Behavioral epigenetic: life experiences, especially early in life have long-lasting effects on behavior. -Epigenetic changes induced by maternal behavior. -Epigenetic effects of early stress in humans. -Epigenetics in cognition.

Effects:

- Epigenetic effects of environmental chemicals -Trans generational epigenetic effects on metabolism. -Epigenetic effects in monozygotic twins.

Steps of DNA methylation maintenance:

---FIRST STEP--- -Prior to replication, CpGs are fully methylated. -The replicated DNA strand is synthesized unmethylated. -Methyltransferase binds to DNA methyl groups. -Any unmethylated DNA is methylated. -Fully methylated DNA is produced. ---LAST STEP---

-----CH21----- How does an epigenetic change differ from a mutation? -A mutation alters the nucleotide sequence in DNA. An epigenetic change does not alter the DNA sequence, but can be inherited by daughter cells. -Epigenetic changes occur due to environmental effects and only persist as long as the environment that induced them remains constant. Mutations are permanent. -Mutations involve nucleotide sequences of only one or a few base pairs. An epigenetic change involves large regions of a chromosome, thousands of base pairs or more in length. -Mutations can be passed on to offspring or to daughter cells. Epigenetic changes cannot be inherited.

-A mutation alters the nucleotide sequence in DNA. An epigenetic change does not alter the DNA sequence, but can be inherited by daughter cells.

Activator proteins increase gene expression, whereas repressor proteins inhibit gene expression. Which statement concerning activator and repressor proteins in eukaryotes is true? -Activators and repressors are only found in prokaryotes. -Repressors are more common than activators in eukaryotes. -Activators and repressors are equally common in eukaryotes. -Activators are more common than repressors in eukaryotes.

-Activators are more common than repressors in eukaryotes.

How do cells regulate gene expression using alternative RNA splicing? -Alternative RNA splicing determines which genes are underexpressed. -Alternative RNA splicing determines which genes are transcribed to mRNA. -Alternative RNA splicing determines how fast certain proteins are degraded. -Alternative RNA splicing determines which proteins are produced from each gene.

-Alternative RNA splicing determines which proteins are produced from each gene.

Effects: Abuse and epigenetics

-Comparison of brains of 24 suicide victims, half of whom had experience childhood abuse. -Adults that had been abused as children had more methylation of glucocorticoid receptor gene, involved in stress response.

Prokaryotic gene regulation

-DNA does not contain introns. -Some genes are organized into operons, and mRNA transcripts often specify more than one protein. -mRNA can be transcribed from DNA and translated into protein at the same time

All of the cells in the human body contain the same genes. How do cells have different morphologies and functions when they contain the same genetic information? -Different cell types receive different endocrine signals. -Different cell types express particular genes at different levels. -Different cell types obtain different types of nutrients from their surroundings. -Different cell types synthesize proteins at a different rate.

-Different cell types express particular genes at different levels.

Genomic imprinting occurs when gene expression in the offspring depends upon whether a particular allele was inherited from the mother or the father. Which statement is likely to explain the evolutionary basis for the existence of imprinting? -Sexual selection favors opposite characteristics in males and females. For example, a deep voice decreases a human female's chances of finding a mate, but does not harm a male's chances. Therefore, the gene for a deep voice is expressed when inherited from the father and not when inherited from the mother. -Sex-linked traits are more likely to affect males than females. Therefore, if a trait is beneficial, it may be expressed only when inherited from the father. Both beneficial and harmful traits may be expressed when inherited from the mother. -Intermediate levels of gene product are ideal for some traits. Homozygous individuals could produce dangerously high levels of gene product. Therefore, it is beneficial if the gene is expressed only when inherited from one parent. This prevents the amount of gene product from rising to a high level by silencing one gene copy in homozygotes. -Maximum fitness can be achieved in different ways for males and females. For example, maximum birth weight and fetal growth are favored by fathers because they increase offspring survival. Mothers favor maternal survival and the preservation of resources for future reproduction. Therefore, a mother may benefit from reduced fetal growth rates.

-Maximum fitness can be achieved in different ways for males and females. For example, maximum birth weight and fetal growth are favored by fathers because they increase offspring survival. Mothers favor maternal survival and the preservation of resources for future reproduction. Therefore, a mother may benefit from reduced fetal growth rates.

Effects: Maternal care and epigenetics

-Mice receiving more maternal care have different patterns of DNA methylation -Expression of stress-response genes altered -Less as adults.

Select the best example of transgenerational epigenetic inheritance. -Individuals with a history of childhood abuse have more methylation of the glucocorticoid receptor gene than individuals without such history. -Vinclozolin binds to insulin receptors, disrupting glucose metabolism and causing epigenetic methylation of the insulin receptor gene. -A long non‑coding RNA transcribed from the Xist gene suppresses transcription of one X chromosome in each female mammal cell. -Experimental rats with nutrient‑restricted diets were at greater risk of infection than control rats that were fed a nutritionally‑complete diet. -Offspring of rats with high‑fat diets were fed a low‑fat diet and had normal weights, but still developed symptoms of diabetes.

-Offspring of rats with high‑fat diets were fed a low‑fat diet and had normal weights, but still developed symptoms of diabetes.

Certain behavioral traits in humans are believed to be encoded by the X chromosome. Examples of such traits include verbal ability and seeking social interactions. For these traits, research has shown that there is less variability between identical male twins than between identical female twins. Which phenomenon best explains these results? -Males have one X chromosome and it is not active. -One X chromosome is randomly inactivated in females. -Male twins both get the same mitochondria from their mother. -Females have double the amount of X expression so there's more room for error.

-One X chromosome is randomly inactivated in females.

-One method to clone a mammal involves nuclear transfer, in which a somatic cell nucleus from a donor mammal is transferred to a recipient egg cell with its nucleus removed. This method results in few live births overall due to a high prevalence of developmental abnormalities. Notably, the probability of a live birth is significantly greater for embryos cloned from the nuclei of undifferentiated embryonic stem cells than for embryos cloned from the nuclei of differentiated somatic cells (Rideout et al., 2001). Select the best explanation of why embryos cloned from undifferentiated embryonic stem cells have greater developmental success than embryos cloned from differentiated somatic cells. -Long non‑coding RNA transfers with the donor nucleus, which represses expression of autosomal genes important to embryonic development. -Somatic cells are older than stem cells and have accumulated mutations that disrupt normal embryonic development. -Patterns of epigenetic markers are different in stem cells and somatic cells, with stem cells having epigenetic patterns more closely associated with early development. -Patterns of epigenetic markers in stem cells and somatic cells are identical, indicating that the observed difference is not due to epigenetic regulation of development. -Embryos not formed from the fusion of a sperm and egg lack genomic imprinting, which increases the likelihood of abnormal embryonic development.

-Patterns of epigenetic markers are different in stem cells and somatic cells, with stem cells having epigenetic patterns more closely associated with early development.

In Arabidopsis thaliana, the Flowering Locus C (FLC) gene codes for a regulatory protein that suppresses flowering. FLC is expressed in seedlings to prevent premature flowering. In mature plants, FLC expression decreases with cooler temperatures, and flowering occurs once sufficiently cool temperatures are reached. If small‑interfering RNA (siRNA) that is complementary to FLC mRNA is introduced, how would RNA interference (RNAi) affect flowering? -RNAi would degrade FLC mRNA and repress flowering. -RNAi would bind irreversibly to FLC mRNA and stimulate flowering. -RNAi would induce methylation of chromatin and repress flowering. -RNAi would degrade FLC mRNA and stimulate flowering. -RNAi is found in prokaryotes and would not affect Arabidopsis.

-RNAi would degrade FLC mRNA and stimulate flowering.

21.3 Processes leading to Epigenetic Changes

-change in chromatin structure, which alter gene expression -Molecular mechaniesm that alter chromatin struture: -Changes in patterns of DNA methylation -Chemical modification of histone proteins -RNA molecules that affect chromatin structure and gene expression.

Why are some stem cells referred to as totipotent? -Totipotent stem cells cannot replicate but can differentiate to become any type of cell in a multicellular organism. -Totipotent stem cells can replicate indefinitely but can only differentiate into one type of cell in a multicellular organism. -Totipotent stem cells can become specialized into one of a limited number of different types of cells in a multicellular organism. -Totipotent stem cells can differentiate into all tissues such that any daughter cell can become any type of cell in a multicellular organism.

-Totipotent stem cells can differentiate into all tissues such that any daughter cell can become any type of cell in a multicellular organism

Processes: Epigenetics effects by RNA molecules

-X inactivation by Xist - RNA coats one of the 2 X chromosomes in females, resulting in silencing.

Place the molecular processes in order that cause one X chromosome in each female cell to be active and the other X chromosome to become inactivated. Not all processes will be used. Active X chromosome

-Xite expression promotes Tsix expression -Xist expression is suppressed

Monozygotic twins have identical DNA sequences, yet twins can differ in some physical or behavioral traits. What evidence suggests that epigenetic effects may cause these phenotypic differences in monozygotic twins? -Younger twins have more similar DNA methylation and histone acetylation patterns than older twins. -Older twins increase DNA methylation, whereas younger twins increase histone acetylation. -Older twins have more similar DNA methylation and histone acetylation patterns than younger twins. -Younger twins increase DNA methylation, whereas older twins increase histone acetylation.

-Younger twins have more similar DNA methylation and histone acetylation patterns than older twins.

DNA can undergo many types of modifications. One of these is methylation. Which bases are methylated more often in human DNA? -cytosine -guanine -adenine -thymine

-cytosine

Eukaryotic gene regulation

-mRNA transcripts typically specify one protein. -A 5 cap and a 3' poly‑A tail are added to mRNA. -Transcription occurs in the nucleus, whereas translation occurs in the cytoplasm.

How can microRNAs (miRNAs) regulate gene expression? -prevent transcription by binding to RNA polymerase and stopping RNA production -prevent translation by binding to mRNA and degrading the mRNA strand -prevent translation by binding to tRNA and interfering with protein synthesis -prevent transcription by binding to DNA and inhibiting transcription factors

-prevent translation by binding to mRNA and degrading the mRNA strand

Which description applies to post‑translational gene regulation? -mRNA modifications such as additions of a 5′5′ cap and 3′3′ poly‑A tail and removal of introns -a gene cluster controlled by a single promoter that transcribes to a single mRNA strand -protein modifications such as addition of a functional group, or structural changes such as folding -processing of exons in mRNA that results in a single gene coding for multiple proteins -heritable changes in gene expression that occur without altering the DNA sequence

-protein modifications such as addition of a functional group, or structural changes such as folding

Modifications to chromatin can affect transcriptional activity by changing the accessibility of DNA to the transcription machinery. The given descriptions are examples of various processes that may or may not cause remodeling of chromatin. Match each description to the effect it has on transcriptional activity caused by chromatin remodeling. 1.Activates

Histone acetyltransferases attach acetyl groups to the N‑terminus of histones.

2.Inactivate

Histone deacetylases remove acetyl groups from the N‑terminus of histones.

3.Activates and inactivates

Histone methylation occurs at different amino acids.

a gene that controls the expression of one or more genes by promoting or inhibiting transcription

Regulatory gene

a regulatory protein that blocks transcription by binding to the operator site

Repressor

Chromatin remodeling

bind directly to DNA sites and reposition nucleosomes

Bacterial repressor

binds to an operator downstream of the promoter site and blocks RNA POLYMERASE.

a molecule that activates mRNA synthesis by disabling the protein that prevents transcription

inducer

an element that disrupts the signal between enhancers and promoters

insulator

Processes:Histone modifications

more than 100 differnetmodification of histo proteins (methylation, acetylation, etc)

a short DNA sequence that can be recognized by a repressor protein

operator

Histone proteins -bind tightly to DNA and strengthen hydrogen bonds between bases. -interact with transcription machinery to increase gene expression. -regulate transcription by changing their associations with DNA. -stabilize condensed chromosomal DNA during transcription.

regulate transcription by changing their associations with DNA.