Gene Regulation in Eukaryotes II: Epigenetics PDF

Because learning changes everything. ® Chapter 16 Gene Regulation in Eukaryotes II: Epigenetics Genetics: Analysis & Principles EIGHTH EDITION Robert J. Brooker © McGraw Hill LLC. All rights reserved. No reproduction or distribution without the prior written consent o...

Because learning changes everything. ® Chapter 16 Gene Regulation in Eukaryotes II: Epigenetics Genetics: Analysis & Principles EIGHTH EDITION Robert J. Brooker © McGraw Hill LLC. All rights reserved. No reproduction or distribution without the prior written consent of McGraw Hill LLC.  Gene Regulation in Eukaryotes II: Epigenetics © McGraw Hill Courtesy of I. Solovei, University of Munich (LMU). 2  Introduction Chapter 15 considered three general aspects of eukaryotic gene regulation 1. Regulatory transcription factors may activate or inhibit genes 2. Changes in chromatin structure affect gene expression 3. DNA methylation usually inhibits transcription Chapter 16 will consider gene regulation by epigenetic mechanisms © McGraw Hill 3  16.1 Overview Of Epigenetics Epigenetics is the study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible, but do not involve a change in the sequence of DNA Epigenetic inheritance may involve epigenetic changes that are passed from parent to offspring An example is genomic imprinting, described in Chapter 5 However, not all epigenetic changes are passed from parent to offspring © McGraw Hill 4  Molecular Mechanisms That Underlie Epigenetic Gene Regulation Different types of molecular changes underlie epigenetic regulation (see Table 16.1) DNA methylation Chromatin remodeling Covalent histone modification Localization of histone variants Feedback loops These modifications can also be non-epigenetic To be epigenetic, these molecular changes must be passed from cell to cell © McGraw Hill 5  Molecular Mechanisms That Underlie Epigenetic Gene Regulation Type of Modification Description DNA methylation Methyl groups may be attached to cytosine bases in DNA. When methylation occurs near promoters, transcription is usually inhibited. Chromatin remodeling Nucleosomes may be moved to new positions or evicted. When such changes occur in the vicinity of promoters, the level of transcription may be altered. Also, larger-scale changes in chromatin structure may occur, such as those that happen during X-chromosome inactivation in female mammals. Covalent histone modification Specific amino acid side chains found in the amino-terminal tails of histones can be covalently modified. For example, they can be acetylated or phosphorylated. Such modifications may enhance or inhibit transcription. Localization of histone variants Histone variants may become localized to specific positions, such as near the promoters of genes, and affect transcription. Feedforward loop The activation of a gene that codes a transcription factor may result in a feedforward loop in which that transcription factor continues to stimulate its own expression. This mechanism is more common in microorganisms. Tab 16.1 © McGraw Hill 6  Targeting of Genes or Chromosomes for Epigenetic Changes Genes or chromosomes can be targeted for epigenetic regulation in two ways Via transcription factors Via noncoding RNA (a) Targeting a gene for epigenetic modification by a transcription factor Fig 16.1a © McGraw Hill 7  Targeting of Genes or Chromosomes for Epigenetic Changes (b) Targeting a gene for epigenetic modification by a noncoding RNA Fig 16.1b © McGraw Hill 8  cis- and trans-Epigenetic Changes Epigenetic changes may by cis- or trans- cis-epigenetic changes are maintained at a specific site For example, a cis-epigenetic change may affect only one copy of gene but not the other copy trans-epigenetic changes are maintained by diffusible factors, such as transcription factors A trans-epigenetic change affects both copies of a gene © McGraw Hill 9  cis-Epigenetic Changes cis-epigenetic changes are maintained during cell division In subsequent cell divisions, the methylated copy of gene B is always methylated whereas the other copy remains unmethylated. Fig 16.2 © McGraw Hill 10  Two General Categories of Epigenetic Gene Regulation Epigenetic gene regulation may occur as a programmed developmental change Genomic imprinting X-chromosome inactivation Cell differentiation Epigenetic changes may be caused by environmental agents Temperature Diet Toxins Refer to Table 16.2 in your textbook for examples © McGraw Hill 11  Factors that promote epigenetic changes Factor Examples Programmed Changes During Development Genomic Certain genes, such as the Igf2 gene discussed in Chapter 5, undergo different patterns of imprinting DNA methylation during oogenesis and spermatogenesis. Such patterns affect whether the maternal or paternal allele is expressed in offspring. X-chromosome As described in Chapter 5 and later in this chapter, X-chromosome inactivation occurs during inactivation embryogenesis in female mammals. Cell differentiation The differentiation of cells into particular cell types involves epigenetic changes such as DNA methylation and covalent histone modification. Environmental Agents Temperature In some species of flowering plants, cold winter temperatures cause specific types of covalent histone modifications that affect the expression of specific genes the following spring. This process may be necessary for seed germination or flowering in the spring. Diet The different diets of queen and worker bees alter DNA methylation patterns, which affects the expression of many genes. Such effects underlie the different body types of queen and worker bees. Toxins Cigarette smoke contains a variety of toxins that affect DNA methylation and covalent histone modifications in lung cells. These epigenetic changes may play a role in the development of lung cancer. In addition, metals, such as cadmium and nickel, and certain chemicals found in pesticides and herbicides, cause epigenetic changes that can affect gene expression. Tab 16.2 © McGraw Hill 12  16.2 Heterochromatin: Function, Structure, Formation, and Maintenance Chromosomal DNA in eukaryotic cells is packaged into chromatin As a reminder, the general features of eukaryotic chromatin structure are described in Chapter 10: Nucleosomes are the basic unit 146 bp of DNA wrapped around an octamer of histone proteins (H2A, H2B, H3, and H4) Nucleosomes interact in a zigzag manner Loop domains are formed from SMC proteins and CTCFs Chromatin composed of DNA, protein, non-coding RNAs © McGraw Hill 13  Euchromatin and Heterochromatin Euchromatin – chromosomal regions that are not stained during interphase; the loop domains are not tightly packed together Transcriptionally active Occupies a central position in the nucleus Heterochromatin – chromosomal regions that are stained during interphase (G1, S, and G2 phases) Greater level of compaction Inhibitory effect on gene expression Localized along the periphery of the nucleus; attached to nuclear lamina © McGraw Hill 14  Fig 16.3 © McGraw Hill ©Science History Images/Alamy 15  Functional Roles of Heterochromatin Formation The formation of heterochromatin plays different functional roles Gene silencing – inhibition of transcription; may limit access of activators or inhibit other aspects of transcription Prevention of transposable element movement – genes needed for transposition are silenced Prevention of viral proliferation – genes needed to produce more viruses are silenced © McGraw Hill 16  Constitutive versus Facultative Heterochromatin Constitutive heterochromatin – regions that are heterochromatic at the same location in all cell types Facultative heterochromatin – heterochromatin that varies in its location among different cell types The genes that are contained with facultative are usually silenced The genes found in facultative heterochromatin in one cell type (e.g., neurons) are different from the genes found in another cell type (e.g., muscle cells) Allows silencing of genes in a cell- or tissue-specific manner © McGraw Hill 17  Constitutive Heterochromatin Characteristics Chromosomal location – close to centromere or telomere Repeat sequences – generally composed of many short tandemly repeated sequences DNA methylation – highly methylated on cytosines in vertebrates and plants Histone modifications – H3K9me3 common in constitutive heterochromatin in yeast and animals; H3K9me2 in plants © McGraw Hill 18  Facultative Heterochromatin Characteristics Formation is reversible; depends on stage of development or cell type Chromosomal location – multiple sites between the centromere and the telomere Repeat sequences – LINE-type repeats DNA methylation – methylation at CpG islands in gene regulatory regions; silences genes Histone modifications – H3K9me3 also found in facultative heterochromatin; animals also often have H3K27me © McGraw Hill 19  Posttranslational modifications Amino-terminal tails of histone proteins are subject to different posttranslational modifications (PTMs) These PTMs result in changes in chromatin structure, such as heterochromatin formation Specific proteins bind to particular PTMs in nucleosomes via protein domains called reader domains; may have writer, eraser, and/or recruitment domains as well Writer domains – addition of PTMs Eraser domains – remove PTMs Recruitment domains – recruit other proteins, such as chromatin remodelers or chromatin-modifying enzymes © McGraw Hill 20  Fig 16.4 © McGraw Hill 21  Molecular Events Leading to Heterochromatin with Higher Order Structure Heterochromatin formation is thought to involve different types of molecular events Posttranslational modification of histones Binding of proteins to nucleosomes Chromatin remodeling DNA methylation Binding of non-coding RNAs © McGraw Hill 22  Consequences of Molecular Events Leading to Heterochromatin Formation These molecular events result in heterochromatin with the following higher-order (reproducible in 3D) structural features 1. Has closer, more stable contacts of nucleosomes with each other via HP1 2. Forms closer loop domains 3. Binds to the nuclear lamina 4. May undergo liquid-liquid phase separation © McGraw Hill 23  Fig 16.5 © McGraw Hill 24  Consequences of Molecular Events Leading to Heterochromatin Formation 1. Closer, more stable contacts of nucleosomes with each other H3K9me3 recognized by HP1 HP1 bridges nucleosomes; makes them more compact 2. Formation of loop domains SMCs promote loop domain formation CTCFs form a crosslink that stabilizes loops © McGraw Hill 25  Consequences of Molecular Events Leading to Heterochromatin Formation 3. Binding of heterochromatin to the nuclear lamina In eukaryotic cells, inner nuclear membrane is lined by nuclear lamina (NL) – fibrous layer of proteins Lamina-associated domains (LADS) are chromosomal regions associated with NL Organize chromosomes into chromatin territories May be involved in gene repression © McGraw Hill 26  Consequences of Molecular Events Leading to Heterochromatin 1 4. Heterochromatin may undergo liquid-liquid phase separation Phase separation - the process in which a mixture becomes separated into two or more distinct phases with different physical and chemical properties (ex. oil droplets in water) Liquid-liquid phase separation (LLPS) refers to the formation of liquid- like compartments that are formed by macromolecules that become concentrated in a given location and come out of solution The nucleolus, located inside the nucleus, is formed by LLPS Heterochromatin may undergo LLPS © McGraw Hill 27  Liquid-liquid phase separation (LLPS) of heterochromatin The phenomenon of LLPS causes regions of heterochromatin to form droplets Fig 16.6 © McGraw Hill 28  Phases of Heterochromatin Formation Initial formation of facultative and constitutive chromatin occurs in 3 phases: 1. Nucleation – short chromosomal site bound by chromatin-modifying enzymes and chromatin-remodeling complexes 2. Spreading – adjacent euchromatin is turned into heterochromatin 3. Barrier – in interphase chromosomes, spreading stops when it reaches a barrier © McGraw Hill 29  Fig 16.7 © McGraw Hill 30  Passage of Heterochromatin from Cell to Cell After facultative heterochromatin is formed, usually in embryonic development, it is passed from cell to cell This pattern maintains gene silencing in a tissue-specific manner During cell division, the chromosomes in the daughter cells usually have the same pattern of constitutive and facultative heterochromatin as the mother cell © McGraw Hill 31  Fig 16.8 © McGraw Hill 32  Heterochromatin Structure is Maintained During Cell Division Pattern of constitutive and facultative heterochromatin is retained after cell division Multicellular species – heterochromatin patterns established during embryonic development Constitutive - same in all cell types Facultative – cell specific © McGraw Hill 33  Mechanisms to Maintain Epigenetic Marks During and following cell division, heterochromatin structure is maintained by DNA methylation – hemimethylated DNA becomes fully methylated via maintenance methylation Histone modifications – histones recruit chromatin-modifying enzymes and chromatin-remodeling complexes to daughter chromatids DNA polymerase – recruit chromatin-modifying complexes Local chromatin structure – higher-order structure favors reformation of heterochromatin © McGraw Hill 34  Maintaining epigenetic modifications that promote heterochromatin formation during DNA replication 1 Fig 16.9 © McGraw Hill 35  Maintaining epigenetic modifications that promote heterochromatin formation during DNA replication 2 Fig 16.9 © McGraw Hill 36  Heterochromatin in Human Disease Some human diseases are caused by abnormalities in heterochromatin formation ICF syndrome Immunodeficiency, centromere instability, and facial anomalies Can be due to a mutation in a DNA methyltransferase gene Roberts syndrome Prenatal growth defects, craniofacial abnormalities, limb malformations Mutations in a gene for an acetyltransferase © McGraw Hill 37  16.3 Epigenetics and Development Development involves a series of genetically programmed stages in which a fertilized egg becomes an embryo and eventually an adult Many changes that occur during development are maintained by epigenetic regulation Three examples Genomic imprinting X-chromosome inactivation Formation of specific cell types and tissues © McGraw Hill 38  Genomic Imprinting Occurs During Gamete Formation Genomic imprinting is a form of gene regulation in which an offspring expresses the copy of a gene from one parent but not both (Chapter 5) Example: In mammals, only the Igf2 gene inherited from the male parent is expressed The Igf2 gene is de novo methylated during sperm formation but not during egg formation The methylation occurs at two sites: the imprinting control region (ICR) and a differentially methylated region (DMR) © McGraw Hill 39  Genomic Imprinting Occurs During Gamete Formation Methylation inhibits the binding of a protein called the CTC- binding factor, which allows the Igf2 gene to be stimulated by a nearly enhancer. In contrast, CTC-binding factor binds to the unmethylated gene and inhibits transcription by stabilizing a loop © McGraw Hill 40  Fig 16.10 © McGraw Hill 41  X-Chromosome Inactivation X-chromosome inactivation (XCI) occurs during embryogenesis in female mammals (see Chapter 5) The X-inactivation center (Xic) is found on the X chromosome The Xic contains two genes, Xist and Tsix, which are transcribed in opposite directions Prior to XCI, the Tsix gene is expressed on both X chromosomes © McGraw Hill 42  (a) The X-inactivation center (Xic) Fig 16.11a © McGraw Hill 43  X-Chromosome Inactivation At the start of X chromosome inactivation, one of the X chromsomes (the one that will become an inactive Barr body) begins to express the Xist gene The process of choosing the inactive X chromosome is not well understood The Xist RNA binds to Xic and then spreads to both ends of the X chromosome The Xist RNA recruits proteins to this X chromosome that cause it to become a compact Barr body and be inactive with regard to the expression of most genes Some genes on this X chromosome may be expressed to some degree © McGraw Hill 44  The process of X-chromosome inactivation (b) Mechanism of X inactivation during embryonic development in mammals Fig 16.11b © McGraw Hill 45  The process of X-chromosome inactivation (b) Mechanism of X inactivation during embryonic development in mammals Fig 16.11b © McGraw Hill 46  Pioneer Factors Pioneer factors, a category of transcription factors, can recognize and bind to DNA sequences exposed on the surface of a nucleosome Recruit chromatin-remodeling complexes and histone-modifying enzymes that carry out epigenetic changes (histone eviction and covalent modifications); see Figure 16.12 May influence the ability of other transcription factors to bind to enhancer sequences Can decrease the level of DNA methylation by binding to CpG islands, blocking access by DNA methyltransferases Involved in the activation of some genes and the silencing of others © McGraw Hill 47  Pioneer Factors Promote Changes in Cell Fate During Embryonic Development Pioneer factors Play a role in changing chromatin structure, which can have positive or negative effects on transcription Drive a reprogramming of the genome during the initial steps of development Enable some genes to be activated and other to be repressed Work in conjunction with nonpioneer transcription factors to promote cell differentiation May prime certain genes for later expression Are important in differentiated cells in adults Levels of expression vary during different stages of embryonic development and among different cell types © McGraw Hill 48  The Action of Pioneer Factors Fig 16.12 © McGraw Hill 49  Development in Multicellular Organisms Involves Epigenetic Gene Regulation Epigenetic changes occur during embryonic development that are remembered during subsequent cell divisions For example, an embryonic cell may undergo epigenetic changes that will cause its future daughter cells to become muscle cells A specific cell type, such as a muscle cell, will activate specific genes and repress others © McGraw Hill 50  Development in Multicellular Organisms Involves Epigenetic Gene Regulation Two types of competing protein complexes are key regulators of epigenetic changes during development that produce specific cell types and tissues Trithorax group (TrxG)- involved with gene activation Polycomb group (PcG)- involved with gene repression © McGraw Hill 51  Development in Multicellular Organisms Involves Epigenetic Gene Regulation With regard to the polycomb group complex, there are two types: PRC1 and PRC2 Though the mechanism may vary from gene to gene, repression may begin by the binding of PRC2 to a polycomb response element. This leads to trimethylation of lysine 27 on histone H3. © McGraw Hill 52  Development in Multicellular Organisms Involves Epigenetic Gene Regulation PRC1 is then recruited to the gene and may inhibit transcription in three ways 1. Chromatin compaction: PRC1 may cause nucleosomes in the target gene to form a knot-like structure. 2. Covalent modification of histones: PRC1 may covalently modify histone H2A by attaching ubiquitin molecules. 3. Direct interaction with a transcription factor: PRC1 may directly inhibit proteins involved with transcription, like TFIID. © McGraw Hill 53  Fig 16.13 © McGraw Hill 54  Fig 16.13 © McGraw Hill 55  16.5 Epigenetics And Environmental Agents Many environmental agents have been shown to cause epigenetic changes. These include dietary effects as well as toxins in the environment. Examples include Dietary effects on the Agouti gene in mice Development of honeybee queens due to royal jelly Flowering in certain species of plants controlled by cold temperatures © McGraw Hill 56  Epigenetics and Diet The Agouti gene in mice promotes the synthesis of yellow fur pigment. In one strain of mice, a transposable element carrying a promoter is inserted upstream from the Agouti gene; this is called the Avy allele (a) The insertion of a transposable element to create the A vy allele Source: Waterland, Robert A., and Jirtle, Randy L., “Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation,” Molecular and Cellular Microbiology, vol. 23, no.15, August 2003, 5293–5300. Fig 16.15a © McGraw Hill 57  (b) Range in coat-color phenotypes in Avyα mice due to epigenetic changes (b): Source: D.C. Dolinoy et al., “Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome,”Environ Health Perspect. 2006 Apr, 114(4): 567-572. Fig 16.15b © McGraw Hill 58  Epigenetics and Diet When pregnant mice were fed a diet that contained chemicals that tend to increase DNA methylation, the offspring tended to be have darker fur. This result is consistent with the idea that DNA methylation inhibits the Agouti gene © McGraw Hill 59  (c) Effect of diet on coat color Source: Waterland, Robert A., and Jirtle, Randy L., “Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation,” Molecular and Cellular Microbiology, vol. 23, no.15, August 2003, 5293–5300. Fig 16.15c © McGraw Hill 60  The darkness of the coat color correlated with the level of DNA methylation of CpG islands within the transposable element (d) Level of DNA methylation of CpG islands within the TE among mice with different coat colors (a, c, d): Source: Waterland, Robert A., and Jirtle, Randy L., “Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation,” Molecular and Cellular Microbiology, vol. 23, no.15, August 2003, 5293–5300. Fig 16.15d © McGraw Hill 61  Dietary Effects on the Development of Honeybees Female honeybees can be: Queen bees: larger, live for years, and produce up to 2000 eggs each day Worker bees: small, sterile, typically live only for weeks Nurse bees: produce a secretion called royal jelly Bees that eat royal jelly into adulthood become queens Larvae injected with a DNA methyltransferase inhibitor became queen bees © McGraw Hill 62  Fig 16.16 © McGraw Hill © Andia/Alamy 63