CHAPTER 21 Epigenetics, Stem Cells, Cellular Differentiation, and Associated Hereditary Neurological Disorders Bhairavi Srinageshwar*, Panchanan Maiti*,**, Gary L. Dunbar*,**, Julien Rossignol* *Central Michigan University, Mt. Pleasant, MI, United States; **Field Neurosciences Institute, Saginaw, MI, United States OUTLINE Introduction to Epigenetics 323 Histones and Their Structure 325 Epigenetics and Neurological Disorders 326 Epigenetics and the Human Brain 324 Stem Cells 324 Conclusions 335 Eukaryotic Chromosomal Organization 325 References 336 INTRODUCTION TO EPIGENETICS changes are discussed in detail elsewhere [3,4], but are briefly described later as an overview for this chapter. Epigenetics is defined as structural and functional DNA methylation. DNA methylation and some of the changes occurring in histones and DNA, in the absence histone modifications are interdependent and play an of alterations of the DNA sequence, which, in turn, has important role in gene activation and repression during a significant impact on how gene expression is altered development [5]. DNA methylation reactions are cata- in a cell [1]. The term “epigenetics” was coined by the lyzed by a family of enzymes called DNA methyl trans- famous developmental biologist, Cornard Hal Wad- ferases (DNMTs), which add methyl groups to a cytosine dington, as “the branch of biology that studies the causal base of the DNA at the 5’-end, giving rise to the 5’-methyl interactions between genes and their products, which cytosine. This reaction can either activate or repress gene bring the phenotype into being”[2]. Epigenetics bridge expression, depending on the site of methylation and it the gap between the environment and gene expression, can also determine how well the enzymes for gene tran- which was once believed to function independently [3]. scription can access the DNA that is wrapped around the Epigenetic changes can lead to increase or decrease in histone [6]. gene expression, thereby activating and/or deactivating Histone methylation. Trimethylation of lysine at position genes, depending on the nature of the epigenetic con- 4 on histone 3 (H3K4me3) promotes gene transcription trol. Some of the most important histone modifications (i.e., gene activation), whereas trimethylation of lysine include: (1) methylation; (2) acetylation; (3) phosphory- at position 27 on histone 3 (H3K27me3) inhibits gene lation; (4) ubiquitination; and (5) SUMOylation and transcription (i.e., gene silencing). Alternate gene acti- DNA modification, including DNA methylation. These vation and repression promote a balanced dose of gene Handbook of Epigenetics. http://dx.doi.org/10.1016/B978-0-12-805388-1.00021-3 Copyright © 2017 Elsevier Inc. All rights reserved. 323 324 21. EPIGENETICS, STEM CELLS, CELLULAR Differentiation, AND Associated Hereditary NEUROLOGICAL Disorders expression, which is required for those genes involved in The outer layer of the embryo, called ectoderm, forms overall development and maturation of organisms. This the central nervous system, and during the process of ensures that only appropriate genes are turned “ON” development, DNA methylation controls the epigen- and “OFF” at any given point of time [7]. Huntington’s etic mechanisms of the embryonic cells. For example, disease (HD), Parkinson’s disease (PD), and multiple to prevent the differentiation of nonneuronal cells into sclerosis (MS) are some of the diseases that are caused by mature neurons, the proneural genes, as well as gene abnormal DNA methylation pattern. These are discussed which are associated with proteins involved with neu- in more detail in later sections of this chapter. rogenesis, such as the brain-derived neurotrophic factor Histone acetylation. DNA acetylation involves the (BDNF) gene, are silenced by DNA methylation at their acetylation of lysine residue, which is catalyzed by the promoter region. However, DNA remethylation can enzymes, histone acetyltransferases (HATs), and histone take place on a neuronal gene, such as Sox2 [11], which deacetylases (HDACs), which have opposing effects on allows for the selective initiation of neuronal develop- each other. HATs transfer acetyl groups to lysine, whereas ment. Similarly, during initial development of the cor- HDACs remove acetyl groups from lysine. However, tex, the genes involved in the formation of glial cells are presence or absence of an acetyl group (CH3CO) on a suppressed by DNA methylation, promoting the forma- lysine residue alters the charge on the amino acid and tion of more neurons during the early stages of neuro- can decrease the interaction of the N-terminal region of nal development. Eventually, during the later stages of histones with the negatively charged phosphate groups cortical development, the DNA methylation is reversed, of DNA. These events are involved in transformation of leading to the generation of glial cells [12,13]. Some of the condensed chromatin into a more relaxed structure, the genes involved in postnatal neurogenesis are Sox2, which can induce gene expression [8]. Dlx2, Sp8, and Neurog2 and those involved in the for- Histone phosphorylation. Phosphorylation involves addi- mation of glial cells are Sparcl1 and Nkx2-2. It has been tion of phosphate group to threonine, serine, and tyrosine shown that during the differentiation of neural stem residues. Phosphorylation of serine at position 139 on cells (NSCs) or progenitor cells, DNA methylation is histone 2 (H2) occurs as a response to DNA damage dur- facilitated by DNMT3a, which silences the genes Sparcl1 ing cell cycling. This relaxes the chromatin; thereby the and Nkx2-2, leading to the inhibition of glial cell for- proteins or factors responsible for repairing the damaged mation and promotion of mature neuron development regions of the DNA have greater access to the DNA, which from NSCs [14]. It is also believed that the normal aging aids in the recovery of the DNA damage. Moreover, phos- process in humans is associated with modification of the phorylation of threonine and serine residues on histone 3 epigenome in the brain, affecting certain genes related (H3) facilitates regulation of gene expression [9]. Histidine to neurogenesis, especially within the cortex [15]. This phosphorylation is one of the epigenetic modifications process leads to the disruption of synapses, abnormal occurring in the prokaryotic cells and in lower eukaryotes neurotransmission, and is associated to age-related dis- that plays a major role in cell signaling. The histidine is orders [16]. However, a comprehensive description of phosphorylated at the imidazole ring, but occurs only on the epigenetic mechanisms related to aging is beyond those nitrogen atoms that are unprotonated [10]. the scope of this chapter. Histone ubiquitination and SUMOylation. Ubiquitina- tion and SUMOylation are associated with posttransla- tional modifications that regulate transcription of gene Stem Cells and protein translation activities. It is well established Dysregulation of epigenetic mechanisms has a direct that the addition of ubiquitin molecules to proteins facil- impact on gene expression patterns that lead to abnor- itate targeted protein degradation. In addition to ubiqui- mal gene functions, which form the basis of most of the tin, various small ubiquitin-like molecules (SUMO) are genetic disorders (monogenic or polygenic) in humans. observed in cells, known as small ubiquitin-related mod- Environmental stress can also alter epigenetic mecha- ifier. These molecules have activities, which are similar nisms, which could become a cause for the predisposi- to ubiquitin and can attach covalently to those proteins, tion of certain diseases, such as autism, schizophrenia, which are involved in changing chromatin structure and and congenital heart disease [17]. This chapter focuses gene expression [3]. on the role of epigenetics and epigenetic changes that take place during stem cell differentiation, which can be used as a potential therapy for neurological diseases. EPIGENETICS AND THE HUMAN BRAIN Stem cells have a unique property of proliferation, dif- ferentiation, and self-renewal. Stem cell plasticity is an Generation of neurons and glial cells from progeni- important characteristic and is based on the degree of tor cells involve epigenetic mechanisms that take place pluripotency, which is the ability of a cell to differenti- throughout the developmental stages of the brain. ate into another cell lineage. Stem cells can be classified V. Factors INFLUENCING EPIGENETIC CHANGES EPIGENETICS AND THE HUMAN BRAIN 325 TABLE 21.1 An Overview of Various Epigenetic Mechanisms Associated With Neurodegenerative Diseases Neurodegenerative disease Stem cell based therapy Epigenetic mechanism involved with disease HD BM-MSCs Histone 3 (H3) methylation leading to reduced trophic factors [20] PD NSCs DNA methylation leading to metabolic defects [21] RTT iPSCs Point mutations in MeCP2 gene leading to defective epigenetic regulatory molecules [22] SCA UC-MSCs Methylation and acetylation of histone leading to reduced RNA expression [23,24] MS HSCs DNA methylation, histone acetylation and posttranscriptional modification by miRNA leading to compromised immune response [25–27] HD, Huntington’s disease; MS, multiple sclerosis; PD, Parkinson’s disease; RTT, Rett syndrome; SCA, spinocerebellar ataxias. as: (1) totipotent, such as embryonic stem cells (ESCs) chromosomes, and the general hierarchy in the chromo- of the morula, which can be differentiated into any cell somal organization, is needed, which