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MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am OVERVIEW OF EPIGENETICS Date: Time: Room: Lecturer: August 26, 2005 * 9:00 am - 9:50 am * Berryhill 103 Terry Magnuson 4312 MBRB [email protected] 843-6475 *Please consult the online schedule for this course for the definitive date and time for this lecture. Office Hours: by appointment Assigned Reading: This syllabus. Key Concepts vs Supplementary Information: Because this syllabus is meant to replace the need for a Genetics textbook, it contains a mixture of information that is critical for you to know and information that serves to illustrate and explain the key points. I have attempted to emphasize important terms, definitions and concepts in red. Basic Principles: Epigenetics is the organization of the eukaryotic genome within chromatin. This organization is involved in the regulation of gene expression. Two examples of epigenetic regulaton that will be dicussed are autosomal imprinting and X-inactivation. Lecture Objectives: By the end of this lecture, you should: understand that autosomal imprinting is parent of origin gene expression regardless of the sex of the individual. understand that, in females, one of the X-chromosomes is inactivated in each and every cell. 1 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am A. Imprinting: The phenomenon in which there is a differential expression of a gene depending on whether it was maternally or paternally inherited. Paternal imprinting means that an allele inherited from the father is not expressed in the offspring. Maternal imprinting means that an allele inherited from the mother is not expressed in the offspring. B. What is imprinting of genes? There are two copies of every gene in each cell of the body: one copy comes from the mother (the "maternal" copy of the gene on the chromosome copy inherited from the mother) and the other comes from the father (the "paternal" copy of the gene on the chromosome copy inherited from the father). Usually, the information contained in both the maternal and paternal copies of the genes are used by the cells to make these products. In other words, both the maternal and paternal genes are usually active or "expressed" in the cells. However, it is now known that the expression of about 100 of the 30,000 or so genes in the cells depends on whether the gene copy was passed down from the father or the mother. This process, whereby the expression of a gene copy is altered depending upon whether it was passed to the baby through the egg or the sperm, is called imprinting. The term "imprinting" refers to the fact that some chromosomes, segments of chromosomes, or some genes, are stamped with a "memory" of the parent from whom it came: in the cells of a child it is possible to tell which chromosome copy came from the mother (maternal chromosome) and which copy was inherited from the father (paternal chromosome). Thus, genetic imprinting is the term used when the expression of a gene depends on whether it is inherited from the mother or the father. Imprinting "breaks" one of Mendel's laws that genes act the same whether transmitted by either parent. Imprinting was first discovered in corn: kernels are dark purple if the Red gene is inherited from the egg but blotchy lavender if the same gene is transmitted through the pollen. This observation was made in 1910 but not understood. Imprinting is a process whereby the expression of a gene is affected but the DNA sequence of the target gene is not altered. It also represents a reversible form of gene activation that changes from generation to generation. While this is therefore not a common mechanism controlling gene expression in humans, it is nevertheless an important one and provides interesting new insights into the mechanisms of gene expression. Some examples include Igf2, Peg1, Ube3A, Kcnq1, Wt1. Genetic imprinting occurs in the ovary or testis early in the formation of the eggs and sperm. Some genes are imprinted to be switched off or inactive only if they are passed down through an egg cell; others will be inactivated only if they are passed down through a sperm cell. Imprinting will then occur again in the next generation when that person produces his or her own sperm or eggs. Prader-Willi/Angelman syndrome 2 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am When the medical world first learned about Prader-Willi syndrome in 1956, doctors had no idea what caused people to have this collection of features and problems that we now know as PWS. It is only in the past 20 years that researchers have discovered the genetic changes on chromosome 15 that are responsible for the syndrome. In 1981, Dr. David Ledbetter and his colleagues reported a breakthrough discovery: They found that many people with PWS had the same segment of genes missing from one of their chromosomes. They had discovered the deletion on chromosome 15 that accounts for more than half of the cases of PWS. Since then, researchers have made a series of other important discoveries about the genes involved in Prader-Willi syndrome. There are several genetic forms of this complex disorder, and genetic tests exist that can confirm nearly every case Prader-Willi syndrome is caused by lack of expression of paternally contributed gene(s). The maternal genes are silent. -Prevalence: 1:12,000- 15,000 (both sexes, all races) -Major characteristics: hypotonia, hypogonadism, hyperphagia, cognitive impairment, difficult behaviors -Major medical concern: morbid obesity More than one gene is involved in PWS, and these genes are near each other in a small area the long arm of chromosome 15—in a region labeled 15q11-q13. Scientists still don’t know exactly how many genes and which specific ones are involved. During the 1980s, scientists puzzled over why some people who seemed to have PWS did not have a chromosome deletion, and why some people with the chromosome 15 deletion seemed to have a different condition from PWS. The next breakthrough came in 1989, when Dr. Robert Nicholls and fellow researchers announced their discovery that PWS is an example of genetic imprinting. In what scientists call the Prader-Willi region of chromosome 15 (the area where the deletion occurs), there are two or more genes that must come from the baby’s father in order to work. In Prader-Willi syndrome, these critical genes are either missing, or they were not properly imprinted to be turned "on" in the chromosome that came from the father. 3 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am Prader-Willi Syndrome • 75% of PWS cases due to cytogenetic deletion 15q11-q13 of paternal 15 A Not expressed A A X A Angelman Syndrome: Also in the chromosome 15q11-q13 region is one gene that is imprinted to be turned "on" only in the mother’s chromosome. When this gene is missing or not working properly on the mother’s chromosome 15, the result is an entirely different syndrome called Angelman syndrome (AS). This discovery explained the mysterious cases of people who had a chromosome 15 deletion but did not have the characteristics of PWS—their deletion was on the chromosome 15 that came from the mother. Because the genetic errors happen in the same section of chromosome 15, PWS and AS are sometimes called "sister" syndromes even though the disorders are not alike. Clinical characteristics include seizures, gait and movement disorders, hyperactivity, laughter and happiness, speech and language, mental retardation and developmental testing and hypopigmentation. In 1997, a gene within the AS deletion region called UBE3A was found to be mutated in approximately 5% of AS individuals. These mutations can be as small as 1 base pair. This gene encodes a protein called a ubiquitin protein ligase, and UBE3A is believed to be the causative gene in AS. UBE3A is an enzymatic component of a complex protein degradation system termed the ubiquitin-proteasome pathway. This pathway is located in the cytoplasm of all cells. The pathway involves a small protein molecule, ubiquitin, that can be attached to proteins thereby causing them to be degraded. In the normal brain, the copy of UBE3A inherited from the father is almost completely inactive, so the maternal copy performs most of the UBE3A function in the brain. Inheritance of a UBE3A mutation from the mother causes AS; inheritance of a UBE3A mutation from the father has no detectable effect on the child. In some families, AS caused by a UBE3A mutation can recur in more than one family member. 4 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am Angelman Syndrome • Angelman syndrome: severe MR with limited speech; ataxic gait; spontaneously happy affect; seizures • 70% of AS cases due to cytogenetic deletion 15q11-q13 of maternal 15 B B B X B Not expressed Question: How can two alleles be identical (DNA sequence) but one be expressed and the other not. DNA methylation is an epigenetic mechanism that plays an important role in mammalian gene control and represents a general mechanism for maintaining repression of transcription. Genes unnecessary for any given cell's function can be tagged with the methyl groups. The number and placement of the methyl tags provides a signal saying that the gene should not be expressed. There are proteins in the cell that specifically recognize and bind the tagged C's, preventing expression of the gene. As would be expected from something important in determining which genes are used, DNA methylation is essential for the normal development and functioning of organisms. This has been shown by engineering mice that can't make the enzymes that put the methyl tags on DNA, called methyltransferases. These mice die before birth. Problems with the DNA methylation machinery also cause developmental diseases in people. People with mutations causing abnormal function of one of the DNA methyltransferase enzymes called Dnmt3b have a disease called ICF syndrome. These people have abnormal immune systems and other genetic problems. Similarly, abnormalities in one of the proteins recognizing and binding mC (called MeCP2) develop Rett syndrome, a form of mental retardation affecting young girls. Hence, we cannot develop and function normally without DNA methylation. Abnormal DNA methylation plays an important role in other developmental diseases as well. With most genes, it probably does not matter that both copies of the gene (the one from the mother plus the one from the father) are both active. This has been shown to be due to a failure in the establishment of the normal pattern of methyl group tags that 5 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am blocks the activity of one of the copies of the gene. Diseases caused by this type of methylation problem include Prader-Willi syndrome and Angelman's syndrome. Abnormal placement of the DNA methylation tags also develops with aging. The tags can decrease in number in some genes, and increase in others, causing inappropriate decreases or increases in the activity of the genes affected. The changes in the placement of the methyl tags may be responsible for a variety of changes in cellular function that occur during aging. There is also evidence that abnormal placement of the methyl tags may contribute to the development of human lupus. Very frequent abnormal increases or decreases in DNA methylation tags are found in most human cancers and contribute to their development. If the genes affected by abnormal methylation tagging happen to be involved in regulating cell proliferation, uncontrolled cell division can occur, and this uncontrolled cell growth is the problem underlying cancer. Scientists are trying to change the abnormal tags or the effects of these tags as one treatment for cancer and to use these tagging differences in early diagnosis of cancer and in monitoring various treatments of cancer. CpG islands: small stretches of DNA that are characterized by more than 50% CpG’s. The typical CpG content is around 20% because of deamination of 5-methylcytosine. The CpG islands can extend over hundreds of nucleotides and there are approximately 45,000 in the human genome. Over half of the human genes are predicted to be associated with CpG islands and in case of genes showing widespread expression, associated CpG islands are almost always found at the 5’ ends of genes, usually in the promoter region, often extending into the first exon. CpG’s within islands tend to be undermethylated where genes are expressed and methylated in tissues where the gene is not expressed. There are dramatic changes in methylation during development. Male and female germ cells have unique patterns of methylation, almost all of which become demethylated in the preimplantation embryo. De novo methylation occurs in the early postimplantation embryo. Imprinted genes show differential methylation: often the inactive allele is methylated at CpG islands and the active gene is not (there are exceptions where the reverse is true). 6 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am p57Kip2 5’ 293bp (35CGs; -556 to -163) Maternal: active Paternal: inactive CpG Island P M What are the mechanisms that control methylation patterns? Distal Chromosome 7 Imprinted Domain M Nao1/4 P Nao1/4 Kip2 tssc3 tssc5 mash2 mtr Kcnq1 (Kvlqt1) Lit1 tssc4 H19 th tapa1 mtr th ins Igf2 tapa1 Imprinting Control Region (ICR) Delete ICR from paternal chromosome imprint is lost & everything is expressed P Nao1/4 tssc3 Kip2 tssc5 Lit1 mtr mash2 Kcnq1 (Kvlqt1) tssc4 M P th ins Igf2 H19 tapa1 Oocyte Sperm 7 X methylated CpG islands MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am KvDMR1 - ICR (34CpGs): T Maternal G Paternal T T T T T T T G G G G G G G M P Gametic imprint M P Oocyte Embryo Sperm CTCF methylated CpG islands Spread of methylation to establish embryonic imprint Covalent Modification of Histone Tails: Another form of epigenetic modification involves methylation, acetylation and ubiquination of nucleosome histones. For example, a polycomb group complex known as PRC2 methylates lysine 27 on histone H3 and this chromatin modification has been shown to be important for genetic imprinting. X-Chromosome Inactivation is an example of epigenetic regulation of a whole chromosome. Females are born with two copies of the X chromosome in their cells and therefore their cells contain two copies of the X chromosome genes. On the other hand, males have only one copy of the X chromosome in their cells so they only have one copy of the X chromosome genes. X-Chromosome Contains about 5% of the haploid genome. Genes encode house keeping and specialized functions. Completely conserved in gene content between species. It does not encode sex determination or differentiation. In females one of the X-chromosomes is inactivated in each and every cell. [known since 1961] In order to correct this potential imbalance between males and females the cells have a system to ensure that only one copy of most of the X chromosome genes in a female cell are "active". Most of the other X chromosome copy is "inactivated" or switched off. This 8 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am mechanism ensures that only the genes located on the "active" copy of the X chromosome can be used by the cell to direct the production of proteins. In mammals, the X chromosome undergoing the inactivation event is a random choice from one cell to another. Once an X chromosome has been inactivated, it remains inactivated in the daughter cells derived from the original cell. This results in a "mosaic effect" or a "patchwork effect" in the individual and can be demonstrated in humans and other mammals. Demonstration of X-Inactivation Cells are taken from a female who is heterozygous for two different X-linked enzyme polymorphisms. She makes two, different forms (A and B) of the glucose-6-phosphate dehydrogenase (G6PD) enzyme and two, different forms (1 and 2) of the phosphoglycerol kinase (PGK) enzyme. In each case, the different forms of the enzymes are distinguishable by their speed of separation in gel electrophoresis. A plug of fibroblast tissue was removed from the woman and individual cells were cloned such that each clone of cells was derived from a single cell. Each clone was then assayed for the type of G6PD and PGK present. The data is shown in the figure below along with a diagram of her two X chromosomes. Clearly, some clones (1, 4, 6, 7, and 9) have only G6PD A and PGK 2 and some clones (2, 3, 5, and 8) have only G6PD B and PGK 1). These combinations reflect the linkage patterns of the X chromosomes of the female as shown in the figure below at the right. X inactivation affects most of the genes located on the X chromosome but not all. Some genes on the X chromosome have their "partner" or pair on the Y chromosome, such as the gene called ZFK that codes for a protein that is possibly involved in the production of 9 MagnusonAugust 26, 2005 Epigenetics 9:00 – 9:50 am both egg and sperm cells. In male cells, therefore, two copies of these genes would be active in the cell: one on the X and one on the Y chromosome. So in order for the same number of active genes to be operating in females, these special genes on the X chromosome are not switched off so that females also have two copies of these genes available for the cell to use. In addition, one gene called XIST that is thought to control the inactivation process itself, is not switched off. Women who are "carriers" of the faulty genes on their X chromosomes involved in conditions such as Duchene muscular dystrophy and hemophilia, will have some cells in their body in which the faulty gene is activated and in others the correct copy of the gene will be activated. The usual random process of X inactivation means that these women would not show any symptoms due to the faulty gene as there would be enough cells with the correct copy of the gene to produce the necessary protein. However, rarely, some women have more cells where the X chromosome carrying the faulty gene is active so that these women do show some of the symptoms of these disorders. In these rare cases the X - inactivation has been "skewed" rather than random. In other rare cases, women have a structural change of one of their X chromosomes: their X chromosome may be missing a small part (deleted) or rearranged in some way. Usually it is this abnormal X chromosome that is inactivated rather than the correct copy. While this may appear to be a protective mechanism by the cell, it is more likely that the cells where the correct copy is inactivated do not survive because the deleted or abnormal X chromosome would be missing segments of important genes. In other rare cases, women have a special type of chromosome rearrangement in their cells called a translocation where the X chromosome is attached to one of the numbered chromosomes (autosomes). In the cells of these women, on the other hand, it is the correct copy of the X chromosome that is usually inactivated, rather than the translocated, abnormal X. If the translocated chromosome was inactivated, not only would the process "switch off" the X chromosome genes but also those on the autosome that were attached to it. The cells in which the translocated chromosome was inactivated would be missing a large number of important genes located on the autosome and would be unlikely to survive. The mechanism leading to X-inactivation is known to involve a gene called Xist which is active on the X that will be inactivated and inactive on the X that remains active. Xist RNA coats the chromosome that will be inactivated to initiate the process. Chromatin remodeling proteins are then recruited, histones are modified and the CpG islands of many of the promoters of the genes on the inactive X are methylated. 10