Lecture 10 Epigenetics (BIOL 3166)

GENETICS, BIOL 3166 Lecture 10 CH. 12 – “EPIGENETICS”  DEFINITIONS OF EPIGENETICS Epigenetics covers all phenomena that, without affecting the DNA sequence of interest itself, can somehow produce heritable changes – on the the level of how genes are expressed an...

GENETICS, BIOL 3166 Lecture 10 CH. 12 – “EPIGENETICS”  DEFINITIONS OF EPIGENETICS Epigenetics covers all phenomena that, without affecting the DNA sequence of interest itself, can somehow produce heritable changes – on the the level of how genes are expressed and how chromosome functions work 2 EPIGENETIC problems How come keratinocytes only form skin cells? How do different adult stem cells know their fate? How can identical twins have different natural hair colors? How can a single individual have two different eye colors? How can identical twin liter mates show different coat colors? How can only paternal or maternal traits be expressed in offspring? How can females express only one X chromosome per cell? How can acquired traits be passed on to offspring? 3 EPIGENETIC problems 4 Epigenetics of toti-, pluri-, and unipotency 5  Epigenetics of toti-, pluri-, and unipotency Totipotency - ability of a single cell to divide and produce ALL of the differentiated cells in an organism, and example totipotent cells are zygotes. Pluripotency – refers to a stem cell that has the potential to differentiate into any of the three germ layers: endoderm (interior stomach lining, gastrointestinal tract, the lungs), mesoderm (muscle, bone, blood, urogenital), or ectoderm (epidermal tissues and nervous system). Unipotency - the concept that one stem cell has the capacity to differentiate into only one cell type. It is currently unclear if true unipotent stem cells exist. Example - hepatoblasts, which differentiate into hepatocytes 6 Pluripotency vs. unipotency What is the difference between totipotency and pluripotency? This ability to become any type of cell in the body is called pluripotent. The difference between totipotent and pluripotent cells is only that totipotent cells can give rise to both the placenta and the embryo. As the embryo grows these pluripotent cells develop into specialized, multipotent stem cells. 7 Unlike genetic changes, epigenetic changes could be experimentally reversed in certain situations! Dolly: The Cloning of a Sheep https://www.youtube.com/watch?v=uAOmyOGELAA 8 Chromatin structure and how it affects gene expression 10 DNA Methylation and Histone Modifications: Epigenetic Code Me Coordination of DNA methylation and histone modification  Chromosome modifiers: WRITERS, ERASERS AND READERS Modifications of histones in nucleosomes Acetylation - only at lysine, phosphorylation mostly at serine, but both lysine and arginine can be methylated Acetylation of lysine – loss of positive charge, interacts less with the next nucleosome. Methylation preserves charge, can increase or decrease nucleosome binding 16 Modifications of histones in nucleosomes 17 Also – different histone variants! Methylation of Cytosine in DNA 5-Methyl Cytosine in DNA  Cytosine Methylation Maintains Inactive-Condensed Chromatin State Transcription factors RNA polymerase Transcription Acetylation DNA methyltransferase 5-methyl-C Methyl-CpG Histone deacetylase Binding proteins and associated co-repressors Transcription blocked Deacetylation X Chromatin compaction Transcriptional silencing Preservation of DNA methylation: mechanism 23 Critical CpG Sequences in CpG Islands Near Promoters  Critical CpG Sequences in CpG Islands Near Promoters Why C to T mutations are so common in human DNA??? Mutation hot spot: CG sequence The best-known example is the two-base (dinucleotide) sequence CG. In mammals, about 80% of CG dinucleotides are methylated: A methyl group is attached to the cytosine base. A methylated cytosine, 5-methylcytosine, easily loses an amino group, converting it to thymine. The end result is a mutation from cytosine to thymine Surveys of mutations in human genetic diseases have shown that the mutation rate at CG dinucleotides is about 12 times higher than at other dinucleotide sequences. 29 DNA methylation in early development and gametogenesis 30  EXAMPLES OF EPIGENETICS INHERITANCE 32 1. Spreading and epigenetic inheritance of heterochromatin Chromatin remodeling exposes regulatory sequences UAS TATA SWI- SNF compl ex + ATP Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Boundaries of heterochromatin must be maintained Figure 11-23 !"#$%&'('%)*++',%‘-"#.'’ &#/'$%0+#'$%."'#1% 1',%'2'%)3+314%%5.%#$%('*1%."'%)'(.136'1'% *(,%"'.'13)"136*.#(4 A chromosomal re-arrangement that moves white near heterochromatin silences the gene in patches… 2. GENOMIC IMPRINTING GENOMIC IMPRINTING Mendel's experimental work with garden peas established that the phenotype is the same whether a given allele is inherited from the mother or the father. Indeed, this principle has long been part of the central dogma of genetics. Recently, however, it has become increasingly apparent that some human genes, one of the alleles is transcriptionally inactive (no mRNA is produced), depending upon the parent from whom the allele was received. For example, an allele transmitted by the mother would be inactive, and the same allele transmitted by the father would be active. The normal individual would have only one transcriptionally active copy of the gene. This process of gene silencing is known as imprinting, and the transcriptionally silenced genes are said to be imprinted. At least several dozen human genes, and perhaps as many as 200 or so, are known to be imprinted. Imprinted alleles tend to be heavily methylated (in contrast to the nonimprinted copy of the allele, which typically is not methylated). The attachment of methyl groups to 5' regions of genes, along with histone hypoacetylation and condensation of chromatin, inhibit the binding of proteins that promote transcription. It should be apparent that this process is similar in many ways to X-inactivation, discussed earlier in this chapter. 38 GENOMIC IMPRINTING Imprinted alleles tend to be heavily methylated (in contrast to the nonimprinted copy of the allele, which typically is not methylated). The attachment of methyl groups to 5' regions of genes, along with histone hypoacetylation and condensation of chromatin, inhibit the binding of proteins that promote transcription. This process is similar in many ways to X-inactivation 39 GENOMIC IMPRINTING Definition of genomic imprinting: – For some genes, although we have two copies, one on each chromosome, only one copy is active or expressed. – Expression of these genes is variable overall but specific for each gene depending on which parent the gene came from. Established (53, filled arrows) and candidate (120, empty arrows) imprinted genes distribution through the human genome Significance of genomic imprinting – proof! Uniparental diploidy – lethal!!!  Imprinting: how is expression controlled? Imprinting occurs by a pattern of methylation – The copy of the gene to be inactivated is coated with methyl groups. – Methylation prevents that gene from being expressed. – This takes place before fertilization, in the egg and sperm cells and is orchestrated by an imprinting center. Genomic imprinting is a reversible form of gene inactivation but remains consistent/stable through mitosis Epigenetic Imprinting DNA methylation in early development and gametogenesis 45 Methylation Changes During Development CP – critical periods of reprogramming Each chromosome in the egg now has a maternal imprint, each in the sperm a paternal imprint For most genes, we inherit two working copies -- one from mom and one from dad. But with imprinted genes, we inherit only one working copy. Depending on the gene, either the copy from mom or the copy from dad is epigenetically silenced. The epigenetic tags on imprinted genes usually stay put for the life of the organism. But they are RESET during egg and sperm formation. Regardless of whether they came from mom or dad, certain genes are always silenced in the egg, and others are always silenced in the sperm. 48 Establishing sex-specific imprints 49 IMPRINTING Overall result in imprinting: – Allows a gene to be expressed from one allele/the other is methylated and therefore inactive – Expression is parent specific Mechanisms of disease in imprinting disorders include: – Deletion – Imprinting Defect – Uniparental disomy – Gene mutation All mechanisms result in a lack of expression of a gene that should be expressed. Disorders of imprinting: uniparental disomy 51  Uniparental Disomy A unique feature to imprinted conditions is uniparental disomy (UPD): when a child inherits both copies of a chromosome from one parent – Is clinically significant if it involves genes that are imprinting – Increases the risk of autosomal recessive disorders if UPD involves the gene affected. Isodisomy – Inheritance of two copies of the same homolog from the one parent Heterodisomy – Inheritance of two different homologs from one parent Prader-Willi and Angelman Syndromes Deletion of about 4 Mb of the long arm of chromosome 15. When this deletion is inherited from the father, the child manifests a disease known as Prader-Willi syndrome (PWS). The features of PWS include short stature, hypotonia (poor muscle tone), small hands and feet, obesity, mild to moderate mental retardation, and hypogonadism. When the same deletion is inherited from the mother, the child develops Angelman syndrome, which is characterized by severe mental retardation, seizures, and an ataxic gait The deletions that cause PWS and Angelman syndrome are microscopically indistinguishable and affect the same group of genes. 53 GENOMIC IMPRINTING Prader-Willi and Angelman Syndromes Analysis showed that the 4-Mb deletion (the critical region) contains several genes that normally are transcribed only on the chromosome inherited from the father. These genes are transcriptionally inactive (imprinted) on the copy of chromosome 15 inherited from the mother. Similarly, other genes in the critical region are active only on the chromosome inherited from the mother and are inactive on the chromosome inherited from the father. Thus, several genes in this region are normally active on only one chromosome. If the single active copy of one of these genes is lost through a chromosome deletion, then no gene product is produced at all, and disease results. 54 3. X-CHROMOSOME INACTIVATION X INACTIVATION In the 1960s, Mary Lyon hypothesized that one X chromosome in each somatic cell of the female is inactivated. This would result in dosage compensation, an equalization of the amount of X-linked gene products in males and females. The Lyon hypothesis stated that X inactivation occurs early in female embryonic development and that the X chromosome contributed by the father is inactivated in some cells, whereas in other cells the X chromosome contributed by the mother is inactivated. In each cell, one of the two X chromosomes is chosen at random for inactivation, so the maternally and paternally derived X chromosomes are each inactivated in about half of the embryo's cells. Once an X chromosome is inactivated in a cell, it will remain inactive in all descendants of that cell. X inactivation is therefore a randomly determined, but fixed (or permanent), process. Because they have two populations of cells, females are mosaics for X chromosome activity. Males, having only one copy of the X chromosome, are not mosaics but are hemizygous for the X chromosome (hemi means "half"). 57 X INACTIVATION 58 X INACTIVATION The inactivation process takes place within approximately 7 to 10 days after fertilization, when the embryonic inner-cell mass contains no more than a few dozen cells. Inactivation is initiated in a single 1-Mb region on the X chromosome long arm, the X inactivation center, and then spreads along the chromosome. X inactivation is permanent for all somatic cells in the female, but the inactive X chromosome must later become reactivated in the female's germline so that each of her egg cells will receive one active copy of the X chromosome. The number of Barr bodies in somatic cells is always one less than the number of X chromosomes. Normal females have one Barr body in each somatic cell, and normal males have none. Females with Turner syndrome, having only one X chromosome, have no Barr bodies. Females who have three X chromosomes per cell have two Barr bodies in each somatic cell. 60 X INACTIVATION is incomplete Why aren't people with extra (or missing) X chromosomes phenotypically normal? X inactivation is incomplete. Some regions of the X chromosome remain active in all copies. For example, the tips of the short and long arms of the X chromosome do not undergo inactivation. The tip of the short arm of the X chromosome is homologous to the distal short arm of the Y chromosome. In total, about 15% of the genes on the X chromosome escape inactivation, and relatively more genes on the short arm escape inactivation than on the long arm. Some of the X-linked genes that remain active on both copies of the X chromosome have homologs on the Y chromosome, preserving equal gene dosage in males and females. Thus, having extra (or missing) copies of active portions of the X chromosome contributes to phenotypic abnormality. 61 XIC Region Selection of one active X chromosome It is hypothesized that there is an autosomally-encoded 'blocking factor' which binds to the X chromosome and prevents its inactivation. The model postulates that there is a limiting blocking factor, so once the available blocking factor molecule binds to one X chromosome the remaining X chromosome(s) are not protected from inactivation. This model is supported by the existence of a single Xa in cells with many X chromosomes and by the existence of two active X chromosomes in cell lines with twice the normal number of autosomes. 65  Solutions Manual – please, work on the problems to better understand the material and prepare for your exams! (PDF copy posted on Canvas!!!) CH. 12 – Focus on problems #: 19, 21, 23, 30, 31