The Evolutionary Reasons of Epigenetics

Abstract

Epigenetic modifications affecting DNA, RNA, and proteins can alter the functional state of a gene and heavily interfere with gene expression. These processes are typically transient, and the predominant form of inheritance is mitotic, with a small fraction of transgenerational modifications. It is therefore reasonable to ask what forces drive this acquisition in living beings, where certain variations in phenotype do not correspond to changes in the DNA sequence.

1. Evolution: Mutation and Selection

It is universally accepted that the biological evolution of living organisms occurs through processes of mutation and selection, although in recent years other elements have also been recognized as playing a role in shaping evolutionary processes [1]. Genetic material has an intrinsic mutability due to its chemical nature and the mechanisms of duplication, which lead to the formation of new sequence variants. Most of these DNA sequence alterations, whether associated with genetic, regulatory, or structural functions, undergo natural selection.

To simplify the concept as much as possible, genetic variations resulting in more advantageous phenotypes are positively selected, potentially leading to an increase in the fitness of that genotype. Conversely, variations resulting in less advantageous phenotypes are counter-selected.

The theory of evolution, originating from Darwin’s work, was integrated with Mendel’s genetic insights in neo-Darwinism and later refined in the modern synthesis [2]. Currently, molecular data allow us to detail previously unknown mechanisms, providing a clearer link between genotype and phenotype. In addition, they provide more and more details about the coding capacity of the genome.

We now understand how a mutation can alter the DNA sequence and, consequently, the amino acid sequence of a protein, as outlined in the central dogma of molecular biology [3]. While the process of transferring information from DNA to RNA is well understood, the regulatory mechanisms governing this process are not yet fully defined.

Mutations affect both coding and regulatory sequences. This can result in phenotypic changes caused by alterations in DNA sequences that encode either regulatory or structural proteins or non-coding regulatory RNAs. However, when discussing gene regulation, we identify a level of control that is not directly tied to the mutations mentioned above and can be altered without changes to the DNA sequence, the physical basis of mutations. This is the epigenetic level, which represents the functional state of a gene. Below, I outline the molecular details to provide a comprehensive understanding of this level.

2. Molecular Aspects and Gene Expression

2.1. The Initiation of Transcription

The formation of the pre-initiation complex in transcription, which occurs in the eukaryotic nucleus, is an extremely critical process and represents the rate-limiting step for the subsequent initiation of the RNA synthesis process [4,5]. For this reason, a more detailed description of the components of the transcriptional machinery is provided.

2.2. The Transcriptional Machinery

The essential step that initiates the entire process of gene expression is carried out by a complex system of interactions between components of the transcriptional machinery: RNA polymerase, initiation factors, and regulatory elements [4,5]. These interactions are influenced in different cell types by the contribution of DNA elements proximal and distal to the transcription start site, DNA sequences like promoters, control elements such as heat shock elements (HSE), glucocorticoid responsive elements (GRE), or stress responsive elements (STREs), and enhancers [6]. All these components, encoded within the DNA sequence, are subject to changes if a mutation affects the sequence that specifies a protein element or alters the regulatory element in the DNA. Such mutations can impact transcription both functionally and in terms of regulation.

Since the regulation of gene expression begins with the initial step of transferring information from DNA to RNA (transcriptional regulation) and subsequently unfolds through systems involving additional levels of control (post-transcriptional regulation), the events occurring during gene transcription are fundamentally critical for all genetic expression processes.

Still focusing our attention on the components at the beginning of transcription, these are entirely under the genetic code control and, as such, are subject to the Darwinian forces of mutation and selection.

Starting in the 1940s, the term epigenetics began to describe a set of processes acting above the genetic level, which respond to environmental variations [7]. Epigenetic processes can be considered responsible for variations in the expression of genetic information that do not involve changes in the DNA sequence and, therefore, may not be strictly subject to Darwinian selection mechanisms. However, as we will see, even though this system primarily operates at the somatic level, the mutation-selection relationship remains intact. Although the system’s sensitivity to environmental factors might suggest otherwise, the principles of evolutionary dynamics still apply.

3. Spatial Containment of DNA

Since it was understood that DNA must be accommodated within the nucleus of a eukaryotic cell through a system that makes it compact and organized, the role of this structural organization in interfering with the transcriptional process has become increasingly evident. Its importance has grown significantly over time [8].

To fit a long DNA molecule into a small compartment, the DNA must be maximally compacted while still capable of fulfilling its role as the repository of genetic information. This information must remain accessible to the transcriptional machinery for expression.

DNA organization involves winding DNA around histone protein cores to achieve compaction and regulation within the cell nucleus in structures known as nucleosomes [9]. Each nucleosome consists of approximately 147 base pairs of DNA wrapped around a histone octamer, which includes two copies of each core histone: H2A, H2B, H3, and H4. Linker DNA, typically around 10–50 base pairs long, connects adjacent nucleosomes, and histone H1 helps stabilize the structure [10]. This arrangement forms the “beads-on-a-string” structure [11], which is further compacted into higher-order chromatin structures to fit the DNA into the nucleus while allowing regulated access for transcription and other processes.

4. The Problem of Transcription Machinery Access to DNA

Since the mid-1980s, both theoretical considerations and increasingly sophisticated experimental approaches have suggested that the genetic information encoded in DNA is not directly accessible to the transcriptional machinery. In vitro transcription experiments indicated that access to DNA is hindered by the histone component of chromatin [12,13]. Later, thanks to the work of Wolfram Horz, it was established that the level of nucleosomal organization could be altered depending on the transcriptional activity [14].

The concept of chromatin remodeling emerged [15], initially referring to physical modifications such as nucleosome displacement from promoters. Subsequent studies by David Allis [16] and Michael Grunstein [17] revealed that these modifications could also be chemical, involving changes to histones associated with DNA. These changes include modifications like acetylation, methylation, phosphorylation, and others [18].

Additionally, complex machineries capable of physically rearranging chromatin were identified. These remodeling machines can slide, expel, and reposition nucleosomes or replace histones with variant forms [19]. This process involves an array of writers (enzymatic factors that introduce modifications), erasers (enzymes that remove epigenetic markers), and readers (factors that recognize and interpret these modifications) [20].

All these processes, which are genetically controlled, regulate DNA transcription, leading to either transcriptional activation or silencing without altering the DNA sequence.

5. Molecular Aspects of Epigenetics

Since the early 2000s, a vast amount of data have accumulated, describing, establishing, and affirming that histone modifications and DNA methylation represent a control level over gene expression that is fundamental. It can rightly be considered the primary basis of epigenetic regulation of gene expression.

5.1. Control of Chromatin Structure

How is chromatin modified or rearranged according to cellular needs? In the 2010s, studies on histone epigenetic modifications revealed a close link between gene expression and the external environment, particularly nutrient intake and cellular metabolism [21]. All the chemical residues responsible for histone modifications are intermediates of cellular metabolism. For example, acetyl-CoA is a precursor for acetylation [22], S-adenosyl methionine for methylation [23], ATP for phosphorylation, and other intermediates contribute to various modifications discovered over time [24].

Thus, deficiencies or surpluses of these precursors can directly impact whether the genome tends toward transcriptional activation or silencing. Yeast experiments have shown that nutrient availability influences the transcription of specific genes [22]. Similarly, in mammals, nutrient fluctuations help regulate circadian rhythms, closely tied to periods of higher or lower metabolic activity depending on the time of day [25].

This connection between precursor availability and histone modifications introduces a window for environmental influence on gene expression. These components do not vary genetically but respond directly to environmental availability. These mechanisms operate differently across contexts of development, differentiation, and environmental conditions.

The ability of the epigenetic machinery to quickly adapt transcriptional responses to environmental changes makes it an exceptionally significant, though often underappreciated, evolutionary advantage.

5.2. DNA Methylation

As early as the 1970s, another chemical modification of DNA was considered important: methylation of cytosines at the 5th position [26]. This methylation, forming 5-methylcytosine, is mediated by DNA methyltransferase enzymes, which are genetically controlled and therefore subject to classical Darwinian selection. DNA methylation influences transcription and serves roles in cellular development and differentiation, as well as maintaining genomic stability, such as through the methylation of coding regions and repetitive sequences. It also partially controls transposon mobility [27].

Like histone modifications, hypo- or hypermethylation processes are influenced by environmental factors. Examples include the metabolism of S-adenosyl methionine, temperature changes, exposure to toxic substances, and even learning or stress. These factors are linked to changes in DNA methylation in specific genes, affecting their expression.

6. Three-Dimensional Nuclear Organization

Regarding DNA in its chromatin form, the nucleosome is the first level of compaction. However, to fit into the nucleus, chromatin undergoes further compaction, is organized into loops anchored to the nuclear matrix, and is folded into higher-order structures [28].

Although our knowledge of these higher-order structures remains limited, advanced techniques [29] that detect DNA sequences in close three-dimensional proximity (despite being distant on the linear sequence) have begun to shed light on how three-dimensional organization can influence transcription. This structural organization of chromatin adds yet another layer of epigenetic control [30].

7. Epigenetic Control, Phenotypic Plasticity, and Evolution

When we observe, through experimental evidence, the activity of the transcriptional machinery and its regulatory components, we are referring to interactions between the DNA molecule (the repository of information) and other informational molecules. According to the central dogma, information flows from DNA to RNA and then to proteins in a sort of one-way direction for most living cells. Information moves from DNA to RNA using the same code, and then to proteins that retain in their sequence the information encoded in the DNA. So far, we have focused solely on the transcriptional aspect, but RNA and proteins, derived directly or indirectly from DNA, also play a significant role. Mutations affecting coding or regulatory sequences result in alterations in protein function or regulatory mechanisms, ultimately impacting the phenotype. Such changes can be positively selected or counter-selected through the processes that determine whether a mutation becomes fixed in the genome and subjected to environmental selection.

This involves both the transcriptional machinery and regulatory components, which include enzymes and RNA. However, as noted, there are windows of communication with the environment that can modify regulation without involving mutations. The ability to respond to environmental changes requires phenotypic plasticity [31], which cannot, in the short term, be achieved through genomic alterations.

Most epigenetic modifications of DNA and chromatin components are transient and inherited mitotically from one cell to another. Only a limited portion of these modifications are passed on to the next generation (transgenerational epigenetic inheritance) [32], making it challenging to understand how epigenetic mechanisms have been so extensively integrated into eukaryotic cells.

It is evident that a rapid and effective environmental response provides a survival advantage. Although this advantage is predominantly somatic and individual, the acquisition of the epigenetic machinery, not the direct implementation of specific modifications, represents a remarkable evolutionary tool. Thus, while primarily an individual process, if adopted by a population, it can enhance the population’s overall fitness.

8. Epigenetic Modifications as Direct Sources of DNA Mutagenesis

8.1. DNA Methylation

Although DNA is a relatively stable biological molecule, cytosines are subject to spontaneous deamination to uracil. Uracil is removed from DNA by uracil glycosylases, which appear to be present in all living cells. Conversely, the deamination of 5-methylcytosine (5meC) produces thymine, which is not recognized by uracil glycosylases and can therefore lead to C → T mutations. In mammals, most cytosine methylation occurs in CpG dinucleotides. Since the deamination of 5meC is thought to be time-dependent, it represents a potential source of mutations that can contribute to the senescence of cells and individuals. However, regardless of the precise nature of the underlying mechanism, the rate of CG → TG transitions (and CG → CA on the other strand) suggests that the hyper-mutability of 5mC may represent a significant force for sequence divergence [33,34].

8.2. DNA Association with Histones

DNA organized with histones into nucleosomes interacts less directly with regulatory, repair, and recombination proteins. This histone-mediated DNA protection reduces the mutation frequency in these regions. The tighter the DNA-histone association, the greater the protection against mutagenesis. Conversely, epigenetic modifications such as histone acetylation, which loosen this association, can increase mutagenesis potential in those regions [35,36].

8.3. Transposons and Insertional Mutations

Transposons, which are variably distributed throughout eukaryotic genomes, undergo extensive epigenetic modifications. In particular, DNA methylation reduces their mobility [37]. Heterochromatization, achieved through chromatin modification, also epigenetically silences transposons. Transposon mobilization induces insertional mutations, aberrant recombination events, and alterations in the expression of nearby genes [38].

8.4. Repeated Sequences

Repeated genomic sequences are prone to rearrangements, leading to gene duplications and the formation of new genes. Epigenetic control of recombination in these sequences is crucial for maintaining duplicated genes and creating new genes [39]. This highlights the evolutionary significance of epigenetic mechanisms in genomic stability.

9. Conclusions: Evolutionary Significance of Epigenetics

Beyond examining the evolutionary consequences of epigenetics, such as transgenerational inheritance or the intrinsic mutagenic nature of epigenetic modifications, it is essential to consider the evolutionary rationale and selective forces that underpin this regulatory level. Epigenetics acts on the execution of the genetic program rather than directly altering it (Figure 1).

Over evolutionary time, organisms have developed mechanisms that use chemical modifications of histones and DNA to modulate gene regulation. This regulation extends beyond transcriptional control to involve a vast array of non-coding RNAs and post-translational protein modifications. Together, these processes provide phenotypic plasticity, enabling an adaptive response in gene expression.

This adaptiveness and plasticity allow organisms to respond to environmental pressures in the short timeframes necessary for individual survival and optimization, acting in turn on the population. This underscores the vital role of epigenetics in eukaryotic evolution.