epigenetics

define epialleles

Alleles that do not differ in their base sequence but have epigenetic differences that produce heritable variations in phenotypes

Which allele has a more open chromatin, B-1 or B'

B-1

what do methyltransferases and demethylases do and how do they affect transcription?

Cells repress and activate genes by methylating and demethylating cytosine bases. Enzymes called DNA methyltransferases methylate DNA by adding methyl groups to cytosine bases to create 5-methylcytosine. - represses transcription Other enzymes, called demethylases, remove methyl groups, converting 5-methylcytosine back to cytosine- activates transcription

which gene highlights the difference between queen bees and worker bees

Dnmt3 gene

Explain the effect that RNA molecules have on chromatin structure and gene expression

Evidence increasingly demonstrates that RNA molecules play an important role in bringing about epigenetic effects. · The first discovered and still best understood example of RNA mediation of epigenetic change is X inactivation, in which a long noncoding RNA called Xist suppresses transcription on one of the X chromosomes in female mammals. · Another example involves paramutation in corn, in which an epigenetically altered allele, by means of siRNAs, induces a change in another allele that then gets transmitted to future generations. Various mechanisms are involved in epigenetic changes produced by RNA molecules. In the case of X inactivation, the Xist RNA coats one X chromosome and then attracts PRC2, which deposits methyl groups on lysine 27 of histone H3, creating the H3K27me3 epigenetic mark, which alters chromatin structure and represses transcription. · Other examples of RNA-associated epigenetic phenotypes are produced by siRNA molecules that silence genes and transposable elements by directing DNA methylation or histone modifications to specific DNA sequences. In addition, research has demonstrated that epigenetic processes such as methylation and histone modification influence the expression of microRNAs, which, in turn, play an important role in regulating other genes. · MicroRNAs also control the expression of genes that produce epigenetic effects, such as those encoding enzymes that methylate DNA and modify histone proteins. · How RNA-based epigenetic changes are maintained across cell divisions is less clear, although some apparently involve small RNAs that are transmitted through the cytoplasm.

3 important features of the paramutation phenomenon

First, the newly established expression pattern of the converted allele is transmitted to future generations, even when the allele that brought about the alteration is no longer present with it. Second, the altered allele is now able to convert other alleles to the new phenotype. And third, there are no associated DNA sequence changes in the altered alleles.

define epigenetics

Here, we will use epigenetics to refer to changes in gene expression or phenotype that are potentially heritable without alteration of the underlying DNA base sequence.

explain the importance in combinatorial epigenetic marks in regulating gene transcription

Many of the enzymes and proteins that produce epigenetic marks cannot bind to specific DNA sequences by themselves. · Thus, they must be recruited to specific targets on the chromosome. · Sequence-specific transcription factors, preexisting chromatin marks, and noncoding RNA molecules serve to recruit histone-modifying enzymes to specific sites. Research indicates that single histone modifications, such as those mentioned here, do not individually determine the transcriptional activity of a gene. Rather, it is the combined presence of multiple epigenetic marks that determines the transcriptional activity level. · There is also considerable "crosstalk" between epigenetic marks: one histone mark may affect whether additional marks occur nearby and how they function. · Crosstalk occurs because histone modifications attract enzymes and proteins that modify other histones.

do epigenetic changes alter the DNA base sequence

No

How does the chemical modification of histone acetylation affect chromatin structure and transcription

The addition of acetyl groups to amino acids in the histone tails (histone acetylation) generally destabilizes chromatin structure, causing it to assume a more open configuration, and is associated with increased transcription.

Modification of histones include: (4)

addition of phosphates, methyl groups, acetyl groups, and ubiquitin

define paramutation

an interaction between two alleles that leads to a heritable change in the expression of one of the alleles

three types of molecular mechanisms that change chromatin structure through epigenetics

changes in patterns of DNA methylation chemical modifications of histone proteins RNA molecules that affect chromatin structure and gene expression

what function do the siRNAs have in corn paramutation

convert B-I to B*

Usually, both _____ are methylated so that methyl groups can occur on both DNA strands

cytosines

how are histone modifications maintained

he process by which histone modifications are maintained across cell division is not as well understood as that of DNA methylation. · There is no universal mechanism for maintaining histone modifications; different types of modifications are undoubtedly maintained by different mechanisms. · Several models have been proposed to explain how histone modifications are faithfully transmitted to daughter cells. · During the process of DNA replication, nucleosomes are disrupted, and the original histone proteins are distributed randomly between the two new DNA molecules. · Newly synthesized histones are then added to complete the formation of new nucleosomes. · Some models assume that after replication, the epigenetic marks remain on the original histones, and that these marks recruit enzymes that make similar changes in the new histones. · For example, PRC2, which adds the H3K27me3 epigenetic mark to histones, preferentially targets histones in chromatin that already contains an H3K27me3 mark, ensuring that any new nucleosomes that are added after replication also become methylated. · In this way, the histone modifications can be maintained across cell division. An alternative model, supported by experimental evidence in Drosophila embryos, proposes that the epigenetic marks are lost during replication, but that the enzymes that bring about histone modifications remain attached to the original histones during the replication process and reestablish the marks on the original and new histones after replication is completed.

if the tandem repeats have open chromatin, what color will the corn be?

light colored

define epigenetic marks

modifications in histone tails and DNA that does not involve the base sequence - are associated with the level of transcription

do paramutations change the DNA sequence

nope

how are epigenetic changes induced by maternal behavior

o A fascinating example of behavioral epigenetics is seen in the long-lasting effects of maternal behavior in rats. § A mother rat licks and grooms her offspring, usually while she arches her back and nurses them. § The offspring of mothers who display more licking and grooming behavior are less fearful as adults and show reduced hormonal responses to stress compared with the offspring of mothers who lick and groom less. § These long-lasting differences in the offspring are not due to genetic differences inherited from their mothers—at least not genetic differences in the base sequences of their DNA. § Offspring exposed to more licking and grooming develop a different pattern of DNA methylation than offspring exposed to less licking and grooming. · These differences in DNA methylation affect the acetylation pattern of histone proteins. · The altered acetylation pattern persists into adulthood and alters the expression of the glucocorticoid receptor gene, which plays a role in hormonal responses to stress. The expression of other stress-response genes is also affected. § To demonstrate the effect of altered chromatin structure on the stress responses of the offspring, researchers infused the brains of young rats with a deacetylase inhibitor, which prevents the removal of acetyl groups from histone proteins. · After infusion of the deacetylase inhibitor, differences in DNA methylation and histone acetylation associated with maternal grooming behavior disappeared, as did the difference in responses to fear and stress in the young rats when they reached adulthood. · This study demonstrates that the mother rat's licking and grooming behavior brings about epigenetic changes in the offspring's chromatin, which causes long-lasting differences in their behavior.

how are stem cells different from induced pluripotent stem cells?

o All cells in the human body are genetically identical, and yet different cell types exhibit remarkably different phenotypes—a nerve cell is quite distinct in its shape, size, and function from an intestinal cell. These differences in phenotypes are stable and are passed from one cell to another, despite the fact that the DNA sequences of all the cells are the same. o Stem cells are undifferentiated cells that are capable of forming every type of cell in an organism, a property referred to as pluripotency. As a stem cell divides and gives rise to a more specialized type of cell, the gene-expression program of the cell becomes progressively fixed, so that each particular cell type expresses only those genes necessary to carry out the functions of that cell type. Though the control of these cell-specific expression programs is not well understood, changes in DNA methylation and chromatin structure clearly play important roles in silencing some genes and activating others. Stem cells provide a potential source of cells for regeneration of tissues, medical treatment, and research. In the past, embryos were the only source of stem cells with the capacity to differentiate into adult tissues, but because of ethical concerns about creating and using human embryos for harvesting stem cells, researchers have long sought the ability to induce adult somatic cells to dedifferentiate and revert to stem cells. Such cells are called induced pluripotent stem cells (iPSCs). Researchers have now successfully created iPSCs by treating fibroblasts (fully differentiated human connective-tissue cells) in culture with a cocktail of transcription factors (Figure 21.12), although less than 1% of the cells that are so treated actually revert to iPSCs. Transcription factors that induce pluripotency cause extensive epigenetic reprogramming, altering the patterns of DNA methylation and histone modifications that accumulate with cell differentiation. Recent research has shown, however, that iPSCs retain a memory of their past and are not completely equivalent to embryonic stem cells (those derived from embryos). One study found that although the DNA methylation patterns of iPSCs differ greatly from those of differentiated somatic cells, the iPSCs retained some methylation marks of the somatic cells, and the methylation of iPSCs was not identical with that of embryonic stem cells. Another study compared histone modifications of fibroblasts, iPSCs, and embryonic stem cells. The iPSCs and embryonic stem cells had many fewer H3K27me3 and H3K9me3 marks than did the fibroblasts, but researchers also found significantly more of these marks on the iPSCs than on the embryonic stem cells

how are epigenetic changes a factor in cognition

o COGNITION A number of research studies have shown that abnormalities in DNA methylation are associated with disorders of development and intellectual ability in humans. § These findings prompted researchers to look for effects of chromatin structure on learning, memory, and cognitive ability in mice and rats. § One study found that training mice to avoid an aversive stimulus at a specific location reduced DNA methylation of the Bdnf gene, which encodes a growth factor that stimulates the growth of connections between neurons. § When demethylated, the Bdnf gene was more active. § When researchers injected a drug that inhibits demethylation into the brains of the trained mice, activity of the Bdnf gene was decreased, and the mice's memory of where the adverse stimulus occurred also decreased. o Another study found that a drug that promotes the acetylation of histone proteins improved learning and memory in mice that have a disorder similar to Alzheimer disease. § Recall that acetylation of histones alters chromatin structure by loosening the association of DNA with histone proteins and stimulates transcription of many genes. o Other studies have found that histone acetylation decreases with age in mice, resulting in diminished expression of genes related to learning and memory. o When researchers injected mice with a drug that is an inhibitor of deacetylase activity, acetylation of histones increased, transcription of genes involved in memory increased, and the memory of the mice improved. These studies suggest that changes in chromatin structure may be involved in memory and learning

what is genomic imprinting?

o Diploid organisms usually possess two alleles at each autosomal locus, one allele inherited from the mother and one allele inherited from the father. For most genes, both alleles are expressed, and the effect of a particular allele on the phenotype is independent of which parent transmitted the allele to the offspring. However, for a few genes, the sex of the parent that contributed the allele influences how that allele is expressed—alleles inherited from the mother and from the father are not equivalent (Figure 21.13). This phenomenon, in which the sex of the parent that transmits the allele determines its expression, is termed genomic imprinting. For some imprinted genes, when the allele is inherited from the male parent it is expressed, but when it is inherited from the female it is silent; for other genes, when the allele is inherited from the female parent it is expressed, but when it is inherited from the male it is silent. As discussed in Section 5.3, genomic imprinting is thought to be due to different degrees of methylation of the alleles inherited from the two parents. o An interesting example of genomic imprinting involves crosses between a horse and a donkey. A cross between a male donkey and a female horse produces a mule, but a cross between a female donkey and a male horse produces a hinny. Mules and hinnies differ in appearance, physiology, and behavior; for example, hinnies are smaller than mules, have shorter ears, and have stronger legs. Because both mules and hinnies have the same genetic makeup (half donkey and half horse) and differ only in which sex conveys the horse and donkey genes, their differences are thought to be due to genomic imprinting. Studies of RNA from mules and hinnies demonstrate that they do indeed exhibit differential expression of some genes. o Previous research had suggested that the number of imprinted genes was limited, but more recent research suggests that the number is much higher. A study conducted by Christopher Gregg, at Harvard University, and his colleagues found that over 1300 genes in the mouse brain exhibited evidence of genomic imprinting. Many of these imprinted genes were not completely silenced; instead, there was biased expression, with one sex transmitting an allele that was more highly expressed than the allele transmitted by the other sex. Gregg and his colleagues also found that imprinting was highly variable; some genes were imprinted only in certain tissues or at certain times of development. o Genomic imprinting has a number of interesting parallels to X inactivation. Most imprinted genes are located in clusters of 3-12 genes that occur in a discrete region of a particular chromosome. Each cluster contains genes that encode proteins as well as genes that produce noncoding RNA. In each of the well-studied examples, there is an imprinting control region that determines imprinting; deletion of this region destroys the ability to imprint. In addition, the imprinting control region exhibits differences in chromatin modifications between alleles inherited from the male and female parents. Each imprinting cluster contains genes for one or more lncRNAs, which play an important role in imprinting and are themselves imprinted. For example, the gene for insulin-like growth factor 2 (Igf2) in humans exhibits genomic imprinting; the Igf2 allele transmitted from the male parent is expressed, while the Igf2 allele transmitted from the female is silenced (see Figure 5.18). Several lncRNAs produced by other genes in the imprinting control region are required for silencing of the female Igf2 allele in the fetus, although how they bring about repression of transcription is not clear. o Many of the well-studied clusters of imprinted genes are associated with disorders that result from faulty imprinting. Beckwith-Wiedemann syndrome is one such disorder. Children with Beckwith-Wiedemann syndrome exhibit excessive growth during fetal development and early childhood. They also have unusual embryonic malignant tumors. Beckwith-Wiedemann syndrome is associated with imprinting in a cluster of genes on chromosome 11, including the Igf2 gene. Individuals with Beckwith-Wiedemann syndrome often have small deletions on chromosome 11 that interfere with the normal process of imprinting. For example, Igf2 is normally expressed only when inherited from the father, but in some children with Beckwith-Wiedemann syndrome, deletions within the imprinting center lead to expression of alleles from both parents. The result is that too much Igf2 is produced, leading to excessive growth and cancer. Prader-Willi syndrome and Angelman syndrome are disorders that are due to imprinting defects on chromosome 15 (see Section 5.3).

explain mechanism of X inactivation in mammals

o Early in the development of female mammals, one X chromosome in each cell is randomly inactivated to provide equal expression of X-linked genes in males and females. Through this process, termed X inactivation, many genes on the inactivated X chromosome are permanently silenced and are not transcribed. Once a particular X chromosome is inactivated in a cell, that same X chromosome remains inactivated when the DNA is replicated, and the inactivation mark is passed on to daughter cells through mitosis. This phenomenon is responsible for the patchy distribution of black and orange pigment seen in tortoiseshell cats. X inactivation is a type of epigenetic effect because it results in a stable change in gene expression that is passed on to other cells. o A great deal of research has demonstrated that which X chromosome is inactivated within a cell is controlled by a particular segment of the X chromosome called the X-inactivation center, which is 100,000 to 500,000 bp in length. Inactivation is initiated at the X-inactivation center and then spreads to the remainder of the inactivated X chromosome. Examination of the X-inactivation center led to the discovery of several genes that play a role in inactivating all but one X chromosome in each female cell and keeping the other X chromosome active o The key player in X inactivation is a gene called Xist (for X- inactive specific transcript), which encodes a long noncoding RNA (lncRNA) that is 17,000 bp in length (Figure 21.11). As its name implies, this RNA molecule does not encode a protein. Instead, Xist lncRNA coats the X chromosome from which it was transcribed. Xist lncRNA then attracts polycomb repressive complex 2 (PRC2) and, eventually, polycomb repressive complex 1 (PRC1). These proteins produce epigenetic marks, such as H3K27me3, and other histone modifications that repress transcription. Eventually, many CpG dinucleotides are methylated, leading to permanent silencing of the inactivated X chromosome. o In mice, there are two separate inactivation events. Soon after fertilization, when the embryo reaches the eight-cell stage, the X chromosome from the male parent is inactivated, while the maternal X chromosome remains active. This event is called imprinted X-chromosome inactivation. In the developing embryo, the paternal X chromosome is then reactivated during blastocyst maturation. Inactivation occurs again in early development, but now which X is inactivated is random: the X from the male parent and the X from the female parent are equally likely to be inactivated. From this point on, whichever X is inactivated remains silenced through subsequent cell divisions. However, some genes on the inactivated X chromosome escape inactivation and continue to be transcribed. How these genes escape X inactivation is not known. Interestingly, in marsupial mammals, the paternal X chromosome is the copy that remains permanently silenced in all cells. o As mentioned, X inactivation is brought about by the transcription of the Xist gene on the inactive X chromosome to produce Xist lncRNA, which coats the inactive X chromosome and leads to changes in chromatin structure that silence transcription. But what happens on the active X chromosome? Why isn't it coated by Xist RNA and silenced? Although all details of this process are not yet understood, recent research has demonstrated that there are several additional genes in the X-inactivation center that encode other lncRNAs. These lncRNAs help bring about inactivation of the inactive X while not silencing the active X (see Figure 21.10). One of these genes is the Tsix gene, which is transcribed on the active X chromosome. Tsix is antisense to Xist, which means that it overlaps with the Xist gene and is transcribed from the opposite strand (see Figure 21.11), producing a Tsix lncRNA that is complementary to Xist lncRNA. Through several mechanisms, Tsix represses the expression of Xist on the active X chromosome. Another major player is a gene called Jpx, which encodes a lncRNA that stimulates transcription of Xist on the inactive X chromosome. Thus, Xist is controlled by two parallel switches with opposite effects: (1) Jpx stimulates Xist expression on the inactive X chromosome, causing Xist to be transcribed and leading to X inactivation; and (2) Tsix represses Xist on the active X chromosome, causing Xist not to be transcribed on that chromosome and preventing inactivation. Several other genes are also involved. A gene called Xite encodes a lncRNA that sustains Tsix expression on the active X chromosome. o This complex process ensures that in each female cell, one X chromosome is inactivated and one remains active. Scientists have long recognized that X inactivation also involves some type of mechanism that is capable of counting X chromosomes, because all but one X chromosome in each cell is inactivated. Thus, the single X in the cells of an XY male remains active (no X inactivation occurs), and two X chromosomes are inactivated in XXX females

explain the epigenetic effects on metabolism

o In the introduction to this chapter, we saw that nutrition during prenatal development can have effects on health in later life. § These types of epidemiological studies on humans are supported by laboratory studies of mice and rats. In one study, researchers fed inbred male mice either a normal (control) diet or a diet low in protein. They then bred mice in both groups to control females fed a normal diet. The males were then separated from the females and never had any contact with their offspring; their only contribution to the offspring was a set of paternal genes transferred through the sperm. § The offspring were raised and their lipid and cholesterol levels examined. The offspring of males fed a low-protein diet exhibited increased expression of genes involved in lipid and cholesterol metabolism, and a corresponding decrease in levels of cholesterol, compared with the offspring of males fed a normal diet. The researchers also observed numerous differences in DNA methylation in the offspring of the two groups of fathers, although no differences could be found in the methylation patterns of the sperm of the two groups of fathers. These results suggest that epigenetic changes altered the cholesterol metabolism of the offspring, although how the differences in methylation were transmitted from father to offspring was unclear. § In another study, researchers fed male rats a high-fat diet and, not surprisingly, the rats gained weight. The researchers then bred these males to females that had been fed a normal diet. The offspring were also fed a normal diet. The daughters of the male rats on the high-fat diet had normal weight, but as adults they developed a diabetes-like condition of impaired glucose tolerance and insulin secretion. The researchers observed that in the insulin-secreting pancreatic islet cells of the daughters, the expression of 642 genes involved in insulin secretion and glucose tolerance was altered, demonstrating that a father's diet affected gene expression in his daughters.

epigenetic effects on monozygotic twins

o Monozygotic (identical) twins develop from a single egg fertilized by a single sperm that divides and gives rise to two zygotes. Thus, monozygotic twins are genetically identical, in the sense that they possess identical DNA sequences, but they often differ somewhat in appearance, health, and behavior. The nature of these differences in the phenotypes of identical twins is not well understood, but recent evidence suggests that at least some of these differences may be due to epigenetic changes. In one study, Mario Fraga, at the Spanish National Cancer Center, and his colleagues examined 80 pairs of identical twins and compared the degree and location of their DNA methylation and histone acetylation. They found that DNA methylation and histone acetylation in identical twin pairs were similar early in life, but that older twin pairs had remarkable differences in their overall content and distribution of DNA methylation and histone acetylation. Furthermore, these differences affected gene expression in the twins. This research suggests that identical twins do differ epigenetically and that phenotypic differences between them may be caused by differential gene expression.

how are epigenetic changes induced by early stress

o Numerous studies have demonstrated that stress during childhood and adolescence produces a number of adverse effects that persist into adult life. § For example, childhood abuse increases the probability that the child will experience depression, anxiety, and suicide as an adult. I § n one study, researchers examined the brains of 24 people who had committed suicide, half of whom had experienced childhood abuse. § They found that those who had experienced childhood abuse had a greater degree of methylation of the glucocorticoid receptor gene, a gene involved in the stress response, than those who had not. § Although the number of brains studied was small, the study suggests that early childhood stress can indeed cause epigenetic modifications to chromatin structure in humans. o Other studies have demonstrated that gene expression is affected by early life experience. § For example, researchers found that children growing up in a lower socioeconomic environment before the age of 5 showed altered expression of over 100 genes related to immune function as adults. The introduction to Chapter 11 discusses the observation that early childhood stress—in the form of growing up in an orphanage—alters telomere length, a type of epigenetic change. o Research in mice suggests that epigenetic effects of stress may be mediated by small RNA molecules. § In these studies, male mice were subjected to chronic stresses such as the odor of a predator, restraint, or noise. § After they were exposed to the stress, the males were bred to females who had experienced no stress. § Their offspring displayed a blunted hormonal response when stressed by restraint, a response called reduced hypothalamic-pituitary-adrenal (HPA) stress axis reactivity. § Furthermore, these offspring exhibited altered expression of genes involved in the stress response. o The researchers found increased levels of nine miRNAs in the stressed fathers' sperm, which they believed conveyed the blunted hormonal response to the offspring. § To test this hypothesis, they injected copies of these specific miRNAs into mouse embryos whose parents had not been exposed to stressful conditions and implanted the embryos into surrogate mothers. § When these mice grew up, they exhibited the same blunted hormonal response as the offspring of stressed fathers, even though their parents had never been exposed to stressful conditions. § Appropriate controls were included to ensure that the observed effect was not simply due to the injection procedure. § The results demonstrated that miRNAs are involved in the epigenetic transmission of the altered hormonal response across generations. § Using RNA sequencing to examine levels of transcription (see Section 20.2), the researchers also showed that the miRNAs brought about changes in gene expression associated with the altered stress response. Other studies have found that fragments of tRNAs passed through sperm similarly bring about epigenetic effects of diet that are passed from male mice to their offspring

explain how paramutation in corn of the B-I and B' alleles affects the phenotype of the corn

o The b1 locus helps to determine the amount of purple anthocyanin that a corn plant produces. § The locus actually encodes a transcription factor that regulates genes involved in anthocyanin production. § Plants homozygous for the B-I allele (B-I B-I) show high expression of the b1 locus and are dark purple. § Plants homozygous for the B′ allele (B′ B′) show a lower expression of the b1 locus and are lightly pigmented. § However, the DNA sequences of the B-I and B′ alleles are identical. § Genetically identical alleles such as these, which produce heritable differences in phenotypes through epigenetic processes, are referred to as epialleles. o In plants that are heterozygous B-I B′, the B-I allele is converted to B′, with the result that the heterozygous plants are lightly pigmented, just like the B′ B′ homozygotes. § The newly converted allele is usually designated B′*. § Importantly, there is no functional difference between B′ and B′*; the B′* allele is now fully capable of converting other B-I alleles into B′* alleles in subsequent generations. o Research has demonstrated that one of the features required for paramutation at the b1 locus is the presence of a series of seven tandem repeats upstream of the coding sequence for the b1 locus. § The repeats do not encode any protein. § Both the B-I and B′ alleles have these tandem repeats, but the chromatin structure of the two alleles differs: the B-I allele has more open chromatin. § The tandem repeats are required for high expression of the B-I allele and high pigment production. § It has been suggested that the repeats act like an enhancer, stimulating transcription at the b1 locus, but only when the chromatin surrounding the repeats is in an open configuration, as it is in the B-I allele. § The more closed configuration in the B′ allele may prevent the repeats from interacting with the promoter of b1 and stimulating transcription. How the repeats might interact with the B′ allele is not known.

Describe the mechanism of paramutation of the B-I allele to B* in corn (genes involved and function)

o The different chromatin states of B-I and B′ may explain their different levels of expression, but how does the B′ allele convert the B-I allele to B′*? § Although the mechanism is not completely understood, recent research demonstrates that the communication between B′ and B-I probably occurs through the action of small RNA molecules. o The tandem repeats that are required for paramutation encode 25-nucleotide-long siRNAs. § Some siRNAs are known to modify chromatin structure by directing DNA methylation to specific DNA sequences. Geneticists have isolated several genes in corn that are required for paramutation to take place; inactivating these genes eliminates paramutation. § One of these genes is mop1, which encodes an RNA-directed RNA polymerase (an enzyme that synthesizes RNA from an RNA template). · This gene is required to generate the siRNAs encoded by the tandem repeats, although it does not appear to be the enzyme that actually transcribes the DNA copies of the tandem repeats. § Another gene required for paramutation, called rmr1, encodes a chromatin-remodeling protein. § Thus, the current evidence suggests that siRNA molecules convert B-I to B′* and that this conversion involves a change in the chromatin states of the alleles. § Research also shows that transcription of the tandem repeats and generation of siRNAs from them are necessary, but not sufficient, for paramutation, so additional factors must be involved. § It is also not clear how the production of the siRNAs is transmitted across generations.

proteins that add/remove histone modifications

polycomb groups

DNA methylation is often associated with _____ of transcription

repression

what effect do polycomb groups have on transcription how do they do this

repression they alter chromatin structure so that the DNA is not accessible to transcription factors, RNA polymerase, and other proteins involved in transcription.

what important feature of the B-I and B' alleles is required for paramutation

seven tandem repeats

what molecule is produced from the tandem repeats of corn

siRNA

where are the seven tandem repeats of the b1 locus located

upstream of the coding sequence

explain the epigenetic effects of envioronmental chemicals

§ Because some chemicals are capable of modifying chromatin structure, researchers have looked for long-term effects of environmental toxicants on chromatin structure and epigenetic traits. § There has been much recent interest in chemicals called endocrine disruptors, which mimic or interfere with natural hormones. Endocrine disruptors are capable of interfering with processes regulated by natural hormones, such as sexual development and reproduction. One of these endocrine disruptors is vinclozolin, a common fungicide used to control fungal diseases in vegetables and fruits—particularly wine grapes—and to treat turf on golf courses. Vinclozolin acts as an antagonist at the androgen receptor; that is, vinclozolin and its metabolites mimic testosterone and bind to the androgen receptor, preventing testosterone from binding. But vinclozolin and its metabolites do not properly activate the receptor, and in this way, vinclozolin inhibits the action of androgens and prevents sperm production. § In one study, researchers found that exposure of embryonic male rats to vinclozolin led to reduced sperm production not only in the treated animals (when they reached puberty), but also in several subsequent generations. Increased DNA methylation was seen in the sperm of the males that were exposed to vinclozolin, and these patterns of methylation were inherited. This study and others have raised concerns that, through epigenetic changes, environmental exposure to some chemicals might have effects on the health of future generations.

example of how polycomb groups affect chromatin

· For example, polycomb repressive complex 2 (PRC2) adds two or three methyl groups to lysine 27 of histone H3, creating the H3K27me3 epigenetic mark, which represses transcription.

example of a histone methylation that increases transcription

· For example, the addition of three methyl groups to lysine 4 in the H3 histone (H3K4me3; K stands for lysine) is often found near transcriptionally active genes. Methylation of lysine 36 in the H3 histone (H3K36me3) is also associated with increased transcription

Explain the example of DNA methylation in honeybees

· How they differ is in diet: worker bees produce and feed a few female larvae a special substance called royal jelly, which causes these larvae to develop as queens. · Other larvae are fed ordinary bee food, and they develop as workers. · This simple difference in diet greatly affects gene expression, causing different genes to be activated in queens and in workers and resulting in very different sets of phenotypic traits. · How royal jelly affects gene expression has long been a mystery, but research now suggests that it changes an epigenetic mark. · In 2008, Ryszard Kucharski and his colleagues demonstrated that royal jelly silences the expression of a key gene called Dnmt3, whose product normally adds methyl groups to DNA. · With Dnmt3 shut down, bee DNA is less methylated, and many genes that are normally silenced in workers are expressed, leading to the development of queen characteristics. · Kucharski and his colleagues demonstrated the importance of DNA methylation in queen development by injecting into bee larvae small interfering RNAs that specifically inhibited the expression of Dnmt3. · These larvae had lower levels of DNA methylation, and many developed as queens with fully functional ovaries. · This experiment demonstrated that royal jelly brings about epigenetic changes (less DNA methylation), which are transmitted through cell division and modify developmental pathways, eventually leading to a queen bee

how is DNA methylation maintained?

· Methylation of CpG dinucleotides means that two methylated cytosine bases sit diagonally across from each other on opposite strands. · Before replication, cytosine bases on both strands are methylated. · Immediately after semiconservative replication, the cytosine base on the template strand is methylated, but the cytosine base on the newly replicated strand is unmethylated. · Special methyltransferase enzymes recognize the hemimethylated state of CpG dinucleotides and add methyl groups to the unmethylated cytosine bases, resulting in two new DNA molecules that are fully methylated. · In this way, the methylation pattern of DNA is maintained across cell division

example of histone methylation that decreases transcription

· On the other hand, the addition of three methyl groups to lysine 9 in H3 (H3K9me3) or to lysine 20 in histone 4 (H4K20me3) is associated with repression of transcription.

how does the chemical modification of histone methylation affect chromatin structure and transcription

· The addition of methyl groups to histones (histone methylation) also alters chromatin structure, but the effect varies depending on the specific amino acid that is methylated; some types of histone methylation are associated with increased transcription and other types are associated with decreased transcription. · For example, the addition of three methyl groups to lysine 4 in the H3 histone (H3K4me3; K stands for lysine) is often found near transcriptionally active genes. · Methylation of lysine 36 in the H3 histone (H3K36me3) is also associated with increased transcription. · On the other hand, the addition of three methyl groups to lysine 9 in H3 (H3K9me3) or to lysine 20 in histone 4 (H4K20me3) is associated with repression of transcription.

How does DNA methylation suppress gene expression?

· The methyl group of 5-methylcytosine sits within the major groove of the DNA molecule, which is recognized by many DNA-binding proteins. · The presence of the methyl group in the major groove inhibits the binding of transcription factors and other proteins required for transcription to occur. · The 5-methylcytosine also attracts certain proteins that directly repress transcription. · In addition, DNA methylation attracts histone deacetylase enzymes, which remove acetyl groups from the tails of histone proteins, altering chromatin structure in a way that represses transcription