Environmental Influences on the Epigenome Lecture 7-8 PDF

Environmental Influences on the Epigenome Lecture 9 & 10 Dr. Hadil Alahdal  Outline How to modify protein What is Epigenetics How can epigenetics be Current research status expression after influenced by and future directions translation...

Environmental Influences on the Epigenome Lecture 9 & 10 Dr. Hadil Alahdal  Outline How to modify protein What is Epigenetics How can epigenetics be Current research status expression after influenced by and future directions translation environmental factors? Introduction The Epigenome: An Overview Epigenetic machinery influences gene expression [messenger RNA (mRNA)] and subsequent protein expression levels but does not alter primary DNA sequence. Epigenetic regulation allows for an immediate organism- level adaptation to the environment. Three major epigenetic regulators have been described, including: 1. Histone modifications, 2. Cytosine phosphate-guanine (CpG) DNA methylation, 3. Noncoding RNA expression.  Translation DNA RNA Protein How can change Add another variation to Proteome be introduced at Proteins way more than genes post-translation This regulation happens through many prosses, for examples: level? Methylation Acetylation What are Post Phosphorylation Glycosylation Translation This can help in: modifications? Protein folding, stability, localization to cell compartment, function, activation, interaction etc The diversity and complexity of proteins Post-translational modifications tools They are chemical modifications that play a key role in functional proteomics They regulate activity, localization, and interaction with other cellular molecules such as proteins, nucleic acids, lipids, and cofactors. Source: Spoel, S, Journal of Experimental Botany, Vol. 69, No. 19 pp. 4499–4503, 2018  PTMs increase proteome diversity Human genome – 21,000 - 22,000 genes, proteins in the human proteome – over 1 million. Single genes encode multiple proteins through the following mechanisms: 1. Genomic recombination, 2. transcription initiation at alternative promoters, 3. differential transcription termination, 4. alternative splicing of the transcript. PTMs further increase the complexity from the level of the genome to the proteome. Source: https://www.thermofisher.com/kz/en/home/life-science/protein-biology/protein- biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview- post-translational-modification.html Epigenetics Epigenetics is the study of heritable changes in gene function that cannot be attributed to changes to the DNA sequences. These heritable changes are brought about by transcriptional processes and post- transcriptional regulators.  Epigenetics Epigenetic mechanisms known to have profound effects on controlling gene expression include: DNA methylation - biochemical addition of methyl groups (CH3) to cytosines in cytosine-phosphate-guanosine (CpG) dinucleotides that inhibit transcription factors binding to promoters. Chromatin remodeling (histone methylation, acetylation/deacetylation) involves changes to the complex of histones and DNA packed within the nucleus. The structure of chromatin affects the accessibility of the chromatin and transcriptional activities inside a cell. microRNAs small non-protein coding RNA molecules found in plants, animals, and some viruses control the target gene expression post-transcriptionally.  1-DNA methylation Is the addition of a methyl group at the fifth carbon position of the cytosine base. 5-methylcyotine (5-mC) bases are often proximal to guanine CpG methylation and occur within regions of the genome with a high cytosine- guanine (CG) content. These high CG content regions are often referred to as CpG islands. The process of adding methyl groups to cytosine is carried out by the DNA methyltransferase (DNMT) enzyme family. This addition requires the cofactor S-adenosylmethionine (SAM).  DNA methylation Methylation is the biochemical addition of a methyl group (CH3) to the cytosine 5- carbon in cytosine-phosphate-guanosine (CpG) dinucleotides via a methyltransferase enzyme. This covalent modification generally turns off the affected genes by attracting proteins that bind to methylated cytosines and block gene transcription. DNA methylation patterns are passed on to progeny cells by the action of an enzyme called maintenance methyltransferase that copies the methylation pattern on the parent DNA strand to the daughter DNA strand as it is synthesized.  Question How do post-translational modifications like methylation and phosphorylation impact protein functionality? DNA Immediately after DNA replication, each daughter double helix will contain one methylated DNA strand - inherited from the parent double methylation helix - and one unmethylated, newly synthesized strand. The maintenance methyltransferase interacts with these hybrid double helices and methylates only those CG sequences that are base-paired is maintained with a CG sequence that is already methylated.  2-Chromatin remodeling-Histone methylation Histone methylation and demethylation influence the availability of DNA for transcription. Amino acid residues can be conjugated to a single methyl group or multiple methyl groups to increase the effects of modification. Source: https://cnx.org/contents/5cz8bfb2@11/Eukaryotic-Epigenetic-Gene-Regulation Acetylation Acetylation, or the transfer of an acetyl group to nitrogen, occurs in almost all eukaryotic proteins through both irreversible and reversible mechanisms. N-terminal acetylation requires the cleavage of the N-terminal methionine by methionine aminopeptidase (MAP) before replacing the amino acid with an acetyl group from acetyl-CoA by N-acetyltransferase (NAT) enzymes. This type of acetylation is co-translational, in that N-terminus is acetylated on growing polypeptide chains that are still attached to the ribosome. While 80 to 90% of eukaryotic proteins are acetylated in this manner, the exact biological significance is still unclear.  3-Chromatin remodeling-Histone acetylation Acetylation at the ε-NH2 of lysine (termed lysine acetylation) on histone N-termini The histone acetylation and deacetylation is of particular interest due to its role in gene regulation. Acetylation occurs on the lysine residue of histone proteins at the N-terminal tail of lysine and is facilitated by the enzymes - histone acetylases (HATs), or histone deacetylases (HDACs). A single lysine alteration on histones significantly impacts cellular homeostasis including transcription factors, molecular chaperones, and cellular metabolism. Histone acetylation by the HATs and HDACs has a well-established link to aging and various neurological and cardiovascular diseases Source: https://cnx.org/contents/5cz8bfb2@11/Eukaryotic-Epigenetic-Gene- Regulation  Question What are the three major epigenetic regulators, and how do they influence gene expression?  3- microRNAs MicroRNAs, or miRNAs, are small RNA molecules (18-24 pb) that control gene expression by base-pairing with their target mRNAs and affecting their stability and inhibit their translation into protein. Like other RNAs, miRNAs also undergo processing to produce the mature, functional miRNA molecule. The mature miRNA, about 22 nucleotides in length, is packaged with specialized proteins to form an RNA-induced silencing complex (RISC), which patrols the cytosol in search of mRNAs that are complementary in sequence to its bound miRNA. 2-microRNA-directed destruction of mRNA Each precursor miRNA transcript is processed to form a double-stranded intermediate, which is further processed to form a mature, single-stranded miRNA. The mature miRNA assembles with a set of proteins into a complex called RISC, which then searches for mRNAs that have a nucleotide sequence complementary to its bound miRNA. Depending on how extensive the region of complementarity is, the target mRNA is either rapidly degraded by a nuclease within the RISC (shown on the left) or transferred to an area of the cytoplasm where other nucleases destroy it (shown on the right).  miRNAs are important epigenetic regulators of gene and protein expression. miRNAs play a role in developmental processes miRNAs and miRNAs are susceptible to exposure to environmental chemicals. environment miRNAs for example are involved in the pathogenesis of pregnancy-related diseases.  Question How does DNA methylation affect gene expression, and what role does the enzyme DNMT play in this process?  Summary: Epigenetics and the environment Epigenetics is the study of changes in gene expression that occur without alterations to the DNA sequence. DNA methylation is one of the key epigenetic modifications, and it can be influenced by various environmental factors. Several articles explore how environmental exposures can lead to changes in DNA methylation patterns in human populations. The interplay between genetics and epigenetics. Individual genetic variations can influence how a person's epigenome responds to environmental exposures, leading to personalized responses. Epigenetics and the environment Large-scale alterations of processes governing methylation, due to environmental exposure, nutritional status, or disease, are associated with global losses or gains of methylation particularly in early development Global loss of methylation is generally associated with genomic instability and is a common phenotype of aging and cancer Conversely, gains in global levels of methylation, specifically in the placenta, have been associated with developmental defects, including Down syndrome and gestational diabetes Global measures of methylation are assessed using technologies such as LINE1, liquid chromatography–mass spectrometry (LC/MS), and Alu methylation  Current technologies enable the assessment of site- specific methylation, in addition to global methylation. Results of these studies have provided key insights into disease development and susceptibility due to potentially causal marks. Gene-Specific For example, in the mouse study that examined the effects of environmental contaminants and nutritional Methylation supplementation on methylation profiles, found that methylation of the mouse coat color gene, as well as nine other CpG loci, are linked to adult health and disease susceptibility. gene-specific alterations in methylation patterning have been linked to environmental exposures, especially those that occur during the prenatal period.  Gene-Specific Methylation in human The study by Heijmans et al. was the first in a human population to show that alteration of methylation at a single gene locus resulted in changes to disease susceptibility and adult outcomes. The researchers investigated the impacts of prenatal exposure to famine during the Dutch Hunger Winter on insulin growth factor 2 (IGF2) methylation. This methylation was associated with lowered birth weight and a predisposition to obesity and adverse metabolic health outcomes later in life. These data suggest that alterations to DNA methylation that occur during the prenatal window result in later-life disease, supporting the underlying developmental origins of health and disease hypothesis. Transcription factors triggered by environmental exposure influence site-specific methylation (a) Activation of transcription factors in response to an environmental contaminant as a mechanism of cellular defense/adaptation. The binding of the transcription factor may inhibit DNA methyltransferase (DNMT) from accessing the DNA for methylation of a particular gene, resulting in gene-specific hypomethylation. (b) Repression of transcription factors in response to an environmental contaminant. The lack of the transcription factor binding may allow DNMT access to particular genomic locations, resulting in gene-specific hypermethylation. TF, transcription factor; TSS, transcription start site.  Question What are some environmental factors that can lead to changes in DNA methylation? Some ENVIRONMENTAL TRIGGERS FOR DNA METHYLATION ALTERATIONS  Aflatoxin B1 (AFB1) is a mycotoxin that is produced by certain fungi and can contaminate foods such as peanuts, grain, and corn. It is one of the most potent hepatic carcinogens 1-Aflatoxin B1 Studies showed that adults in two separate Taiwanese populations who were exposed to AFB1 had lower levels of methylation in white blood cells. CpG sites related to immune response and growth factors were identified to be altered in association with AFB1 in white blood cells.  2-Air pollution Air pollutants encompass a range of environmental exposures, including particulate matter (PM), ozone, nitrogen oxides, sulfur oxides, carbon monoxide, diesel exhaust fumes, and toxic chemicals like benzene. Epigenome studies are showing associations between exposure to air pollution and changes in DNA methylation levels. Specific pollutants like PM and ozone composition influence gene-specific methylation patterns. PM exposure, is associated with alterations in DNA methylation of specific genes related to blood pressure regulation, inflammation, and other biological processes. Traffic-related air pollution can influence methylation at the tet methylcytosine dioxygenase 1 (TET1) gene, affecting gene expression. Prenatal exposure to air pollution affects methylation patterns differently depending on the timing of exposure during pregnancy. Specific genes related to immune response, metabolism, and vascular development are affected by prenatal air pollution exposure. DNA methylation alterations in peripheral blood related to air pollution is more sever during the prenatal period and childhood.  3-Arsenic 1. Arsenic exposure affects hundreds of millions of people worldwide. 2. Associated with altered methylation patterns in adults and infants, resulting in hypomethylation and hypermethylation. 3. Recent research indicates that the effects of arsenic on DNA methylation may vary by sex, with positive associations in males and negative associations in females. 4. Several studies have examined gene-specific DNA methylation changes in adults and infants exposed to arsenic, with most findings indicating hypermethylation. 5. Some specific genes have been associated with health outcomes related to arsenic exposure, such as lower birth weight, cancer, and diabetes. 6. The literature suggests that arsenic-associated methylation may contribute to genomic instability and the development of arsenic- related diseases, both in cases of prenatal and chronic exposure.  4-Bisphenol-A 1. BPA is a public health concern due to its widespread exposure and unclear health effects. 2. Research indicates that BPA induces hypomethylation in women and young girls, but its effects on males are unclear. 3. Fetal exposure to BPA is associated with nonmonotonic changes in DNA methylation in the liver. 4. BPA alters methylation patterns in various tissues, including the placenta, fetal liver, and fetal kidney. 5. Specific genes affected by BPA include the small nucleolar RNA (SNORD) complex, sulfotransferase family 2A member 1 (SULT2A1), and catechol-O- methyltransferase (COMT). 6. BPA can induce hypomethylation of CpG targets on the X chromosome and affect methylation related to immune function, transport activity, and metabolism.  5-Tobacco smoke 1. Tobacco smoke is a known carcinogen and is associated with cardiovascular disease and chronic respiratory conditions. 2. Tobacco smoke exposure can lead to genomic instability and dysregulation of the epigenome. 3. Both in utero and adult exposures to tobacco smoke have been linked to global hypomethylation. 4. Tobacco smoke exposure also impacts genes related to cancer, cell cycle, metabolism, fetal growth restriction, development, and more. 5. Common genes affected by prenatal tobacco smoke exposure include Contactin-associated protein-like 2 (CNTNAP2), cytochrome P450, family 1, member A1 (CYP1A1), and myosin IG (MYO1G). 6. DNA methylation patterns affected by tobacco smoke exposure remain stable over time. 6-Nutritional Factors 1. Early-life and prenatal nutrition can impact developmental programming and later- life health outcomes. 2. nutrient donors like methionine, folate, betaine, and choline are linked to alterations in DNA methylation patterns, increasing global methylation levels and deficiency causing hypomethylation. 3. Folate, an essential nutrient for fetal development, is associated with global methylation measures in infants, children, and adults. 4. The relationship between methylation and methyl donors is significant during the third trimester of pregnancy. 5. Paternal intake of methyl donor nutrients influences global methylation in offspring and affects infant metabolism and growth. 6. Specific loci in the genome, are influenced by nutritional factors and are linked to later-life health issues such as obesity and diabetes. 7. Good nutrition can moderate the effects of environmental contaminant exposure. 8. Micronutrients like vitamin B family members, homocysteine, choline, vitamin B12, vitamin D, and selenium, are critical for methylation status.  Question What are the major gaps in epigenetics research, and how might addressing these improve our understanding of gene regulation?  Future directions Four Major Gaps: 1. Environmental Mixtures: Nutritional assessment and the assessment of multiple contaminants are necessary to advance the field. 2. Sex-Specific Effects: Differences in methylation patterns between males and females can affect health outcomes and should be considered in future studies. 3. Tissue Specificity: While blood-based methylation is often used as a biomarker for disease, it is important to study specific target tissues and examine tissue-specific changes in methylation marks. 4. Stability and Functional Consequences: Limited research has assessed the stability of methylation over time and its functional consequences. Longitudinal studies with measures of methylation and gene expression are needed to address this gap.  Conclusion There is a dynamic relationship between environmental influences and the epigenome, through exposure-associated DNA methylation This field of research has important implications for understanding the impact of our environment on health and may lead to innovative strategies for disease prevention and personalized medicine. References https://www.annualreviews.org/doi/pdf/10.1146/annurev- publhealth-040617-014629 https://www.sciencedirect.com/science/article/pii/S22147500203036 44 https://www.frontiersin.org/articles/10.3389/fgene.2021.664717/full https://www.sciencedirect.com/science/article/abs/pii/S0024320518 306696