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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
"This book successfully conveys that we are in the early stages of understanding epigenetic phenomena, and McCulley admirably explains why this new discipline is important, even if significant hurdles remain before we understand enough about epigenetics to use that information when designing medical or nutritional/lifestyle interventions." -David S. Moore, The Quarterly Review of Biology, March 2025, Volume 100, Number 1 pp. 43 - 44
An incisive and contemporary discussion of epigenetic phenomena applied to human health and disease
Epigenetics and Health: A Practical Guide delivers a thorough and insightful exploration of the basic principles of gene function, gene regulation, and gene expression. The author explains how epigenetic modifications alter gene expression and demonstrate the role played by environmental factors—including nutrition, exercise, toxins, and stress—in gene regulation, as well as their potential health consequences.
The book presents current methods for analyzing epigenetic variation, including NGS applications and bioinformatic analysis.
Readers will be encouraged to question, analyze, and critically appraise the literature on epigenetics to further develop their understanding. They’ll also find:
- Explorations of epigenetic mechanisms, homeostasis, and the potential for manipulating the epigenome
- Practical discussions of methods for epigenetic analyses
- How to address cancer epigenetics, mental health epigenetics, and guidance on developing an epigenetics research project
Epigenetics and Health: A Practical Guide will benefit practicing geneticists and medical geneticists seeking insights into epigenetic phenomena applied to human health and disease.
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Veröffentlichungsjahr: 2024
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Table of Contents
Cover
Table of Contents
Title Page
Copyright Page
Preface
Overview
1 How Do Genes Work?
1.1 DNA, Genes and Proteins
1.2 Gene Control, Homeostasis and Epigenetics
1.3 DNA Methylation and Regulation of Gene Expression
1.4 Post‐transcriptional Regulation of Gene Expression
1.5 Promoters and Enhancers
1.6 Mutation Genotype, Phenotype, Epigenotype
1.7 Conclusion
Task
Further Reading
2 What is Epigenetics?
2.1 Properties and Functions of Heterochromatin and Euchromatin
2.2 DNA Methylation
2.3 DNA Demethylation
2.4 Chromatin Remodelling: Post‐translational Modifications of Histone Proteins
2.5 Non‐coding RNAs
2.6 Polycomb Proteins
2.7 Conclusion
Task
Reference
Further Reading
3 Epigenetic Mechanisms, Homeostasis and Potential for Manipulating the Epigenome
3.1 Pharmaceutical
3.2 DNA Methylation and Impact on Nutrition
3.3 Diet and Cancer Prevention
3.4 Dietary DNMT Inhibitors
3.5 Dietary HDAC Inhibitors
3.6 Dietary Modulators of ncRNAs
3.7 Precautions and Issues with Dietary Chemoprevention
3.8 Epigenetics and Inflammation/Immune Response
3.9 Epigenetic Inheritance Mechanisms
3.10 X‐inactivation
3.11 Genomic Imprinting
3.12 Transgenerational Epigenetic Inheritance
3.13 Conclusion
Task
References
Further Reading
4 Tissues and Methods for Epigenetic Analyses
4.1 Methods for Assessing Genome‐Wide DNA Methylation‐EPIGENOMICS
4.2 Methods for Assessing Genome‐Wide Histone Modifications
4.3 Integrative Analysis – Looking at DNA Methylation and Histone Modification
4.4 Novel Technologies
4.5 Single‐Cell Approaches
4.6 ncRNAs
4.7 Oxidised DNA Methylation
4.8 Data Analysis
4.9 Conclusion
Task
References
Further Reading
5 Normal and Abnormal Epigenetic Variation
5.1 Epigenetics and Trained Immunity
5.2 Epigenetics and Vascular Senescence
5.3 Epigenetics and Obesity
5.4 Epigenetics and Cumulative Toxin Exposure: Toxicoepigenomics
5.5 Epigenetics, COVID‐19 and Environmental Chemical Exposures
5.6 Case Focus: Rheumatology
5.7 Conclusion
Task
References
Further Reading
6 Cancer Epigenetics
6.1 DNA Methylation and Role in Cancer Development
6.2 Histone Modification and Role in Cancer Development
6.3 Non‐coding RNAs and Role in Cancer Development
6.4 Chromatin Remodelling and Role in Cancer Development
6.5 DNA Damage Response and Role in Cancer Development
6.6 Epigenetics and Metabolic Programming in Cancer
6.7 Summary
6.8 Epigenetic Alterations in Cancer and Therapeutic Design
6.9 Conclusion
Task
Further Reading
7 Mental Health Epigenetics
7.1 Specific Genes of Interest with Regards to Mental Health
7.2 Specifically Focussing on Schizophrenia
7.3 Transgenerational Epigenetic Influences on Predisposition to Psychiatric Disorders
7.4 Suicide/PTSD
7.5 Stress, Epigenetics and Transgenerational Epigenetic Inheritance: Consequences of Inequity/Deprivation
7.6 Conclusion
Task
References
Further Reading
8 Developing a Project
8.1 Considerations for Epigenetic Research
8.2 Conclusion
8.3 Getting Started
Why Do Epigenetic Research? What Do You Want to Achieve?
Reference
Further Reading
Index
End User License Agreement
List of Tables
Chapter 1
Table 1.1 How do you stop a gene from working?
Chapter 2
Table 2.1 Types of epigenetic modifications.
Table 2.2 DNA methylation.
Table 2.3 Histone modifications.
Table 2.4 Table of some of the common histone modifications and their assoc...
Table 2.5 Table summarising some of the several types of non‐coding RNAs (n...
Chapter 3
Table 3.1 Overview of methods used to manipulate the epigenome.
Table 3.2 Impact of nutrients on DNA methylation.
Table 3.3 Potential chemo‐preventative nutrients and their proposed mechani...
Table 3.4 Food compounds reported to inhibit DNMT.
Table 3.5 Food sources reported to impact chemoprevention via HDAC inhibiti...
Table 3.6 ncRNA, dietary modulators and association with cancer.
Table 3.7 Epigenetic mechanisms targeted in treating immune disorders.
Table 3.8 Some known human imprinted genes along with their associated impr...
Table 3.9 Studies on transgenerational epigenetic inheritance.
Chapter 4
Table 4.1 Table summarising common methods used to analyse the epigenome.
Chapter 5
Table 5.1 Overview of life‐course factors that influence the epigenome.
Chapter 6
Table 6.1 Biology of cancer diagram.
Table 6.2 Approaching cancer from an epigenetic perspective.
Chapter 7
Table 7.1 Epigenomics and psychiatry overview.
Chapter 8
Table 8.1 Tissue types and epigenetic research.
Table 8.2 Simplification of linkages between stress, inequity and epigeneti...
Table 8.3 Summary flow diagram of steps involved in planning an epigenetics...
List of Illustrations
Chapter 1
Figure 1.1 The gene is shown in a linear arrangement, with the promoter at t...
Guide
Cover Page
Table of Contents
Title Page
Copyright Page
Preface
Overview
Begin Reading
Index
WILEY END USER LICENSE AGREEMENT
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Epigenetics and Health
A Practical Guide
Michelle McCulley
Otago University
New Zealand
Copyright © 2024 by John Wiley & Sons, Inc. All rights reserved.
Published by John Wiley & Sons, Inc., Hoboken, New Jersey.Published simultaneously in Canada.
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Library of Congress Cataloging‐in‐Publication DataNames: McCulley, Michelle, author.Title: Epigenetics and health : a practical guide / Michelle McCulley.Description: Hoboken, New Jersey : Wiley, [2024] | Includes bibliographical references and index.Identifiers: LCCN 2023049009 (print) | LCCN 2023049010 (ebook) | ISBN 9781119307983 (paperback) | ISBN 9781119307990 (adobe pdf) | ISBN 9781119308003 (epub)Subjects: MESH: EpigenomicsClassification: LCC RB155 (print) | LCC RB155 (ebook) | NLM QU 476 | DDC 616/.042–dc23/eng/20231215LC record available at https://lccn.loc.gov/2023049009LC ebook record available at https://lccn.loc.gov/2023049010
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Preface
Epigenetics is the study of heritable changes in gene expression or cellular phenotype that do not involve changes to the underlying DNA sequence. These changes can be influenced by a variety of factors, including environmental factors, diet and lifestyle, and can have a significant impact on an individual’s health and development. The importance of epigenetics lies in the fact that it provides a mechanism for the inheritance of traits that are not coded for in the DNA sequence itself. Epigenetic modifications can be passed down from one generation to the next and can influence the expression of genes that are involved in a wide range of biological processes, including development, ageing and disease.
Understanding the role of epigenetics is particularly important in the study of complex diseases such as cancer and neurological disorders, as it provides a potential avenue for developing new diagnostic and therapeutic strategies. By identifying specific epigenetic changes associated with these diseases, researchers can develop targeted treatments that can help to mitigate their effects and improve patient outcomes. Overall, the study of epigenetics is essential for gaining a deeper understanding of the complex interplay between genetics and environmental factors in shaping an individual’s health and development and has the potential to revolutionise our understanding of human biology and disease.
This book will explore selected epigenetic phenomena as applied to human health and disease. We will investigate how, through epigenetic mechanisms, our genome is responsive to a wide range of environmental influences including nutrition, toxins and social circumstances. The mechanisms controlling these effects and their phenotypic outcomes will be covered. By the end of the book, the reader should understand the differences between genetic and epigenetic influences on gene expression, the range of epigenetic mechanisms used to regulate gene expression, how epigenetic modifications are propagated, and the phenotypic consequences for health and disease. In this book, the reader will rapidly build their knowledge to develop their understanding of epigenetics to a point where they can apply their learning to formulate a research question that relates to their own specific interest in this contemporary field.
Overview
The first three chapters of this book are designed to think about health issues from an epigenomic perspective, to understand molecular homeostasis and the interplay between genes and the environment. Chapter 4 focuses on tissues, methods, and resources for analysis. Chapters 5–7 focus on specific research areas; the concluding chapter focuses on future research questions and how the epigenome is a target for health and medicine. We end the book with a practical step‐by‐step guide to planning an epigenomics research project.
1How Do Genes Work?
In this chapter, we will discuss fundamental concepts central to molecular biology and to understanding epigenetics. We will briefly discuss DNA, genes and proteins, mutation, genotype and phenotype and the relationships between each, and finally provide an overview as to how genes are controlled, outlining gene regulation and repression. We will outline the concept of molecular homeostasis and the interaction between genome and environment, briefly differentiating between epigenetics and genetics.
1.1 DNA, Genes and Proteins
DNA is comprised of four nucleotide bases: adenine, guanine, cytosine and thymine. DNA is a stable double helix with guanine always pairing with cytosine and adenine always pairing with thymine, or uracil in the case of RNA. The human genome is diploid, so it is comprised of 2 sets of 23 chromosomes, 1 inherited from each parent. Every nucleated cell contains the same 46 chromosomes with the same genetic information – this is our genome. Approximately 10% of the human genome is estimated to be coding, that is, specifically encodes for proteins; the remainder is noncoding DNA including repetitive sequences such as microsatellites, minisatellites, transposable elements (SINES, LINES), satellite DNA and triplet repeats.
Type of region
Description
Protein‐coding genes
Segments of DNA that encode proteins.
Noncoding RNA genes
Segments of DNA that encode RNA molecules that do not translate into proteins. Examples include microRNAs and long noncoding RNAs.
Regulatory regions
DNA sequences that control gene expression, such as promoters, enhancers, silencers and insulators. These regions can be located upstream or downstream of the gene, or even within the gene itself.
Repetitive DNA
Segments of DNA that are repeated many times throughout the genome, such as transposable elements, satellite DNA and minisatellites.
Intergenic regions
DNA sequences located between genes that do not have any known function. These regions make up the majority of the human genome.
Introns
Segments of DNA located within genes that do not encode proteins. Introns are transcribed into RNA but are removed during the process of RNA splicing, which generates the final mRNA transcript that is used to produce proteins.
The human genome project suggests that there are around 20 000 genes, with each human chromosome on average containing 1300 genes. Genes are transcribed and translated to produce their encoded protein. This two‐stage process takes the message embedded in double‐stranded DNA and transcribes the coding sequence as single‐stranded mRNA, which is then translated by the ribosome using tRNA and rRNA to produce the protein. Genes range in size from 1 kb, as in the case of insulin, to 2.5 Mb for larger genes, such as dystrophin. Almost all genes contain introns and exons. Exons are expressed coding regions and introns are non‐expressed intervening sequences. Introns are transcribed into primary RNA and then spliced out of mature RNA in the cytoplasm. The average number of exons for a human gene is 9, and therefore introns are 8. However, there is considerable variation, e.g. 79 for dystrophin and 3 for beta‐globin. The average size of an exon is 145 bp.
In addition to introns and exons, genes also have an adjacent upstream (5′) regulatory promoter region as well as other regulatory sequences such as enhancers, silencers and sometimes a locus control region. The promoter region contains specific conserved sequences such as TATA box, CG box and CAAT box, which provide binding sites for transcription factors. The first and last exons also contain untranslated regions (UTRs) known as the 5′UTR and 3′UTR. The 5′UTR signals the start of transcription and contains ATG, the initiator codon that initiates the site of the start of translation. The 3′UTR contains a termination codon, which marks the end of translation, plus nucleotides that encode a sequence of adenosine residues known as the poly (A) tail; the addition of a poly (A) tail is an essential step in the process of transcription that enables the pre‐mRNA to exit the nucleus and move into the cytoplasm for translation.
Gene regulatory sequence
Function
Promoters
DNA sequences located upstream of the transcription start site that recruit the transcriptional machinery to initiate gene expression
Enhancers
DNA sequences that can be located far away from the gene they regulate and can enhance gene expression by increasing transcription rates and/or making expression more specific to certain cells or conditions
Silencers
DNA sequences that can be located near or far from the gene they regulate and can reduce or turn off gene expression
Insulators
DNA sequences that act as boundaries between different gene regulatory regions, preventing their influence on each other
Scaffold/matrix attachment regions
DNA sequences anchor the chromatin to the nuclear matrix, thereby organising and stabilising the structure of chromatin and regulating gene expression
CpG islands
Regions of DNA that have a high density of CpG dinucleotides are often associated with gene promoters and are involved in the regulation of gene expression through DNA methylation
miRNA target sites
Specific RNA sequences within the 3′ UTR of messenger RNAs that are recognised by microRNAs and lead to translational repression or mRNA degradation
Cis‐regulatory modules
Clusters of enhancers, silencers and promoter sequences that work together to regulate the expression of a specific gene or set of genes in response to different signalling pathways
Pre‐mRNA contains the entire transcribed sequences of exons and introns; the introns must be removed to produce mRNA that comprises the precise code for translation into a functional protein product. The removal of introns occurs through splicing, which occurs in a spliceosome, itself composed of hundreds of proteins and 5 RNAs. Once a transcript has been spliced and its 5′ and 3′ ends modified, a piece of mature functional mRNA has been produced, suitable for translation into a protein. There are specific nucleotide recognition sequences that aid in splicing. These sequences are present: towards the end of an exon, at the beginning of an intron, at the end of an intron, at the beginning of the next exon and at a region within the intron but close to the 3′ end, which provides a binding site for intron removal. Such sequences are recognised by small nuclear ribonucleoproteins (snRNPs), and they cut the RNA at the intron‐exon borders and connect the exons together. Alternative splicing is a mechanism that allows more information to be packed into a single gene. That is, from a single gene, through splicing exons together in different combinations, multiple RNAs and functional proteins can be produced; this allows cells to produce related but distinct proteins from a single gene. For example, one type of protein may be produced in one tissue, whereas another form may be produced in another tissue (Figure 1.1).
Figure 1.1 The gene is shown in a linear arrangement, with the promoter at the beginning, the transcribed region in the middle and the terminator at the end. The transcribed region is shown with a series of exons (which code for protein) separated by introns (which do not code for protein). The regulatory elements, which can be located upstream or downstream of the promoter, are also shown at the beginning of the gene. At the end of the transcribed region, there is a stop codon that signals the end of the protein‐coding sequence.
The estimated 20 000 protein‐coding genes comprising the human genome are spread between the lengths of the human chromosomes. Each gene has a promoter where transcription of mRNA by RNA polymerase II is initiated by transcription factors. There are also remote elements called enhancers that will modulate the activity of the promoter. Different cell types activate gene expression in a different manner by making use of the genome's extensive system of regulatory cis‐acting elements. The mechanisms underlying this process involve physical changes to the chromatin that either promote or inhibit gene expression. This is fundamental to understanding epigenetics, as it is how gene expression is suppressed or enhanced.
1.2 Gene Control, Homeostasis and Epigenetics
In complex multicellular organisms, differential gene expression is fundamental during embryonic development and in the maintenance of the adult state. It is key to understand that different cells make different proteins, which means different genes are switched on in different tissues even though all cells carry the same comprehensive set of genetic instructions. Therefore, there must be a way in which the body controls which gene is switched on, to what extent and when. Unused genetic information is not discorded – just not switched; for this to happen, there are specific mechanisms that can activate specific portions of the genome and repress the expression of other genes. The activation and repression of genetic loci can be seen as a form of molecular homeostasis, a delicate balancing act for a healthy organism, given expression of the wrong gene at the wrong time in the wrong cell type or in the wrong amount can lead to a harmful phenotype even when the gene itself is normal, such as in cancer or cell death.
Housekeeping genes need to be expressed in all types of nucleated cells because they encode a vital product needed to fulfil an important cellular function, for example, protein synthesis, energy production. Many other genes, however, show a much more restricted pattern of expression that is tissue specific. Spatial restriction of gene expression can occur at many distinct levels: multiple organ/tissue, specific tissue/cell lineage/cell type, individual cells and intracellular distribution. Similarly, gene expression is also temporally restricted at various levels: cell cycle stage, developmental stage, differentiation stage and inducible expression.
Gene expression requires two events to occur: first, the recruitment and activation of chromatin remodelling enzymes that alter the structure of the nucleosome and make the promoter sites on the DNA accessible. The second is the recruitment of coactivators to help assemble the factors needed for transcription; this includes transcription factors, RNA polymerase II, etc. Most eukaryotic genes are regulated at the transcriptional level either via the complex interplay between transcription factors, gene promoters and enhancers and/or through epigenetic mechanisms including chromatin remodelling and DNA methylation. Posttranscriptional gene regulation is through the regulation of splicing and mRNA processing, regulation of mRNA transport, degradation of mRNA, translational regulation or by modifying the translated protein to alter its activity.
Chromatin remodelling is essential for many processes including transcription, replication, DNA repair and recombination. Many of these changes are mediated by chemical changes to the N‐terminal tails of core histones in a nucleosome. The histone tails are exposed on the surface of the nucleosome and are amenable to modification through acetylation, phosphorylation and methylation, allowing access to the underlying DNA. Acetylation adds an acetyl group to specific lysine residues; acetylated histones are found in regions of open chromatin where transcription occurs, which allows transcriptional enzymes to have access to the DNA. Acetylation is mediated by histone acetyltransferases (HATS) and deacetylation by histone deacetylases (HDACs) – both important to gene expression.
1.3 DNA Methylation and Regulation of Gene Expression
The DNA of most eukaryotes is modified after replication through the addition of methyl groups to bases and sugars. Base methylation most often involves enzyme‐mediated addition of methyl groups to cytosine; in most eukaryotes, approximately 5% of cytosine residues are methylated; however, the extent of methylation can be tissue specific and can vary from less than 2% to over 7%. In eukaryotes, low amounts of methylation are associated with elevated levels of gene expression and elevated levels of methylation are associated with low levels of gene expression. In mammalian females, the inactivated X chromosome has a higher level of methylation than the active X chromosome. Methylation patterns are tissue specific and, once established, heritable for all cells of that tissue. The precise mechanism as to how methylation affects gene regulation is still uncertain. It is possible that there are proteins that bind to the methyl group attached to the cytosine; these proteins could recruit corepressors or HDACs to remodel chromatin, changing it from open to closed.
1.4 Post‐transcriptional Regulation of Gene Expression
As outlined above, primary mRNA resulting from transcription is then further modified prior to translation – noncoding introns are removed, exons are spliced together and mRNA is modified through 5′ cap and poly A tail, prior to export to the cytoplasm for translation. Whilst many opportunities exist for further regulation during these steps, the major two are alternative splicing and regulation of the stability of the mRNA itself. Alternative splicing can generate multiple forms of a protein, so the expression of one gene can produce a family of related proteins.
Post‐translational regulation
Mechanism
Examples
Protein phosphorylation
Addition of phosphate group to serine, threonine or tyrosine residues
Activation of Cyclin‐dependent kinase 1 during cell cycle progression
Protein methylation
Addition of methyl group to arginine or lysine residues
Histone methylation by EZH2 in Polycomb repressive complex
Protein acetylation
Addition of acetyl group to lysine residues
Histone acetylation by histone acetyltransferases (HATs) in chromatin remodelling
Protein ubiquitination
Addition of ubiquitin to lysine residues
Ubiquitination of tumour suppressor p53 leading to its degradation
Protein sumoylation
Addition of small ubiquitin‐like modifier (SUMO) protein to lysine residues
SUMOylation of transcription factor Sp3 leading to repression of its activity
Protein neddylation
Addition of NEDD8 to lysine residues
Neddylation of Cullin proteins leading to activation of Cullin‐RING E3 ubiquitin ligases
Protein glycosylation
Addition of carbohydrate to serine, threonine or asparagine residues
Glycosylation of E‐cadherin promoting its adhesive function in cell–cell junctions
Protein lipidation
Addition of lipid group to cysteine residue
Palmitoylation of Hedgehog protein for proper signalling in development
1.5 Promoters and Enhancers
Transcription in eukaryotes is controlled through the interactions of promoters and enhancers; there are other localised sequence‐based elements such as the CCAAT box, which also have an important regulatory effect and are found closer to the gene itself within the promoter region. Enhancers control the rate of transcription and can be located before, after or within the gene expressed. Transcription factors are proteins that bind to DNA‐recognition sequences within promoters and enhancers and then activate transcription through protein–protein interaction. A gene can have different methylation patterns in different tissues and will be correlated with different regulatory patterns.
As mentioned previously, there are two types of regulatory sequences that control gene transcription: promoters and enhancers. Promoters are the recognition point for RNA polymerase binding; they are located immediately next to a gene, typically several hundred nucleotides long and need to be able to allow binding of RNA polymerase II to transcribe primary mRNA. The promoter region has several key elements that aid in its recognition by the polymerase enzyme; the promoter itself – the TATA box (made of 8‐bp consensus sequence only AT base pairs), typically flanked either side by GC‐rich regions. Many promoters also contain CAAT box and GC box‐ both bind transcription factors and function like enhancers‐ mutations in either can affect the rate of transcription. RNA polymerase II requires transcription factors to aid in the start of transcription; they are assembled at the promoter in a specific order and provide a platform that RNA polymerase II can recognise and bind to. The organisation of the upstream region of a gene including the promoter region is variable with respect to the nature, number and arrangement of controlling elements, in some cases including sites for enhancer binding and tissue‐specific enhancer binding.
Enhancers can be on either side of a gene, so upstream (5′) or downstream (3′), they can also be at a reasonable distance from the gene or even within the gene itself. If they are adjacent to the gene, they are termed cis‐regulators, as opposed to trans regulators such as binding proteins, which can regulate a gene on any chromosome. Typically, enhancers will interact with multiple regulatory proteins and transcription factors to increase the rate of transcription efficiency or promoter activation. Within enhancer sites, it is common to find binding sites for both positive and negative gene regulators. The main difference between enhancers and promoters is that enhancers do not have a fixed position (i.e., can be upstream, downstream or within the gene they regulate); the orientation of the enhancer can be inverted without significant effect on its action, and if an unrelated gene is placed near an enhancer, the transcription of that gene becomes enhanced. Enhancers are responsible for time‐ and tissue‐specific expression. They exert their effect when the transcription factor binds to the enhancer, altering the chromatin configuration, and second, through binding/looping DNA, they bring distant enhancers and their promoters into direct contact to form complexes with transcription factors and polymerases. The new resulting configuration increases the overall rate of RNA synthesis.
1.6 Mutation Genotype, Phenotype, Epigenotype
Now we understand the structure and function of a gene, which is to carry instructions to produce a specific protein, we can begin to understand what the consequences are of mutations to DNA and disruptions to normal control over gene expression, that is, the switching on and off of a gene. In the simplest terms, the DNA spanning a particular area of a chromosome will contain the information needed to produce a particular protein in response to a signal to do so. If there are disruptions or changes to the DNA sequence of a particular gene, then this can have an impact on how or even whether the protein is produced. Given the complexity of transcription and translation, including the splicing of introns, exons and mechanisms that control gene expression, there are multiple locations where this can have a detrimental effect in terms of influencing the production of a protein. The resulting physical/physiological effect or the effect on a person’s health is termed the phenotype; the change to the DNA is termed the genotype. There are also changes to the gene control mechanisms external to the DNA; these are termed epigenotypes.
What then is the significance of mutation? Are all mutations equal? Fundamental to molecular pathology is trying to understand why a particular genetic/epigenetic change or genotype should result in a specific phenotype or clinical condition. When trying to understand mutation, we can take a tiered approach, with the first stage being to ascertain whether the mutation results in loss of function or gain of function. With a loss of function, the protein product will have reduced or no functional capability. With a gain of function mutation, the protein product will do something atypical or unusual. Deletions of a whole gene, nonsense mutations and frameshifts are almost certain to destroy gene function. Mutations that change conserved sequence flanking introns affect splicing and will typically knock out the function of the gene; splicing can be changed by many other sequence changes too. Missense mutation is more likely to be pathogenic if it affects a part of the protein that is known to be functionally important, for example, a DNA‐binding domain. Changing an amino acid is more likely to affect function if that changed amino acid happens to be conserved in related genes. Amino acid substitutions are more likely to affect function if they are non‐conservative.
We will first look at the main classes of DNA mutations, which are deletions, insertions, frameshifts, dynamic mutations and single base substitutions (including missense mutations, nonsense mutations and splice site mutations). If we look at these from the perspective of how you stop a gene from working, then it can help to determine what meaningful interpretations of such data are. Genetic variants can also have an impact on epigenetic mark; single SNPs can have an impact on more than one proximal CpG sites. Correlation between SNPs and methylation is referred to as mQTLs – methylation quantitative trait loci. The added complexity is that SNPs can affect both gene expression and methylation independently, as outlined in Table 1.1.
1.7 Conclusion
Virtually any disease is the result of the combined action of genes and the environment, but the relative role of the genetic component may be large or small. For many of the common diseases affecting humans, such as diabetes, heart disease and cancer, there is not a single gene responsible. We are complex organisms, and as such, our pathophysiology is often a combined effect of what we inherit and our individual environment or circumstances.
