DNA Methylation- Definition, Principle, Significance, Control

DNA is the molecule that carries the genetic information of living organisms. It consists of four types of nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C). These nucleotides form complementary base pairs (A-T and G-C) and are arranged in a double helix structure. The sequence of nucleotides in DNA determines the expression of genes, which are the units of heredity that control various traits and functions of cells.

However, gene expression is not only influenced by the DNA sequence, but also by chemical modifications that occur on the DNA molecule itself or on the proteins that bind to it. These modifications are called epigenetic changes, and they can affect how genes are turned on or off without altering the DNA sequence. Epigenetic changes can be inherited from one cell generation to the next, or they can be induced by environmental factors such as diet, stress, or exposure to toxins.

One of the most common and well-studied epigenetic modifications is DNA methylation. This is a process by which a methyl group (-CH3) is attached to a specific position on a cytosine base, usually when it is followed by a guanine base (a CpG site). DNA methylation can affect the accessibility and binding of transcription factors and other proteins that regulate gene expression. Depending on the context, DNA methylation can either repress or activate gene expression.

DNA methylation is essential for normal development and differentiation of cells in multicellular organisms. It plays a key role in various biological processes such as genomic imprinting, X-chromosome inactivation, and silencing of repetitive elements. It also helps to maintain genomic stability and prevent mutations. Abnormal DNA methylation patterns have been associated with many diseases, especially cancer.

In this article, we will explore the definition, principle, significance, and control of DNA methylation in more detail. We will also discuss some of the current challenges and opportunities in DNA methylation research and its applications in medicine and biotechnology.

DNA methylation is a type of epigenetic modification that involves the addition of a methyl group (-CH3) to a DNA base, usually cytosine. This alters the physical and chemical properties of the DNA molecule, and can affect its interaction with other molecules, such as proteins and RNA. DNA methylation can also influence the accessibility and stability of the DNA, and thus regulate its transcriptional activity.

DNA methylation occurs predominantly at CpG dinucleotides, which are regions where a cytosine is followed by a guanine on the same DNA strand. CpG sites are often clustered in regions called CpG islands, which are typically located near gene promoters or enhancers. The methylation status of CpG islands can influence the binding of transcription factors and chromatin modifiers, and thus modulate gene expression.

DNA methylation can also occur at non-CpG sites, such as CHH or CHG (where H is any base except G), especially in plants and embryonic stem cells. The function and regulation of non-CpG methylation are less well understood, but may be involved in genome stability, chromatin structure, and gene silencing.

DNA methylation is catalyzed by a family of enzymes called DNA methyltransferases (DNMTs), which transfer a methyl group from S-adenosylmethionine (SAM) to the 5-carbon position of cytosine, forming 5-methylcytosine (5mC). There are three main types of DNMTs in mammals: DNMT1, DNMT3A, and DNMT3B. DNMT1 is responsible for maintaining the methylation pattern during DNA replication, while DNMT3A and DNMT3B are involved in establishing new methylation marks during development or in response to environmental stimuli.

DNA methylation is not a static process, but rather a dynamic one that can be reversed by various mechanisms. One of them is passive demethylation, which occurs when DNMT1 fails to copy the methylation mark to the newly synthesized DNA strand during replication, resulting in the loss of methylation over time. Another mechanism is active demethylation, which involves the removal of the methyl group by enzymes such as TET (ten-eleven translocation) or AID/APOBEC (activation-induced deaminase/apolipoprotein B mRNA editing enzyme complex). Active demethylation can occur in specific contexts, such as during embryogenesis, reprogramming, or cellular differentiation.

DNA methylation is an important epigenetic mechanism that contributes to the regulation of gene expression and genome function in various biological processes and diseases. It is influenced by both genetic and environmental factors, and can be inherited across generations or altered by external stimuli. Understanding the molecular mechanisms and biological implications of DNA methylation is essential for advancing our knowledge of human health and disease.

DNA methylation is a biochemical reaction that involves the transfer of a methyl group from a donor molecule, such as S-adenosylmethionine (SAM), to a specific target site on the DNA molecule. The target site is usually a cytosine nucleotide that is followed by a guanine nucleotide, forming a CpG dinucleotide. The methyl group is covalently attached to the 5-carbon atom of the cytosine ring, resulting in 5-methylcytosine (5-mC). This reaction is catalyzed by a family of enzymes called DNA methyltransferases (DNMTs), which have different roles and specificities in the genome.

There are two types of DNA methylation: de novo methylation and maintenance methylation. De novo methylation refers to the establishment of new methylation patterns in previously unmethylated regions of the genome, such as during embryonic development or cellular differentiation. De novo methylation is mediated by DNMT3a and DNMT3b, which can recognize and methylate CpG sites regardless of their methylation status. Maintenance methylation refers to the preservation of existing methylation patterns during DNA replication and cell division. Maintenance methylation is mediated by DNMT1, which preferentially recognizes and methylates hemimethylated CpG sites, where only one strand of DNA is methylated. This ensures that the daughter cells inherit the same methylation patterns as the parent cells.

DNA methylation can also be reversed by a process called demethylation, which involves the removal of methyl groups from 5-mC. Demethylation can occur passively or actively. Passive demethylation occurs when DNMT1 fails to methylate hemimethylated CpG sites during DNA replication, leading to the gradual loss of methylation over several cell divisions. Active demethylation occurs when 5-mC is enzymatically converted to other modified bases, such as 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), or 5-carboxylcytosine (5-caC), by a family of enzymes called ten-eleven translocation (TET) proteins. These modified bases can then be recognized and excised by base excision repair (BER) enzymes, resulting in the restoration of unmethylated cytosine.

The process of DNA methylation is dynamic and regulated by various factors, such as DNA sequence, chromatin structure, transcription factors, non-coding RNAs, and environmental stimuli. DNA methylation can affect gene expression by altering the accessibility of DNA to transcriptional machinery and by recruiting or repelling proteins that bind to methylated DNA or histones. DNA methylation can also influence other epigenetic modifications, such as histone modifications and chromatin remodeling, creating a complex network of interactions that shape the epigenetic landscape of the genome.

Gene expression is the process by which the information encoded in DNA is converted into functional molecules, such as proteins and RNAs. Gene expression is regulated by various factors, including transcription factors, chromatin structure, and epigenetic modifications. DNA methylation is one of the most studied epigenetic modifications that can affect gene expression.

DNA methylation can influence gene expression in different ways, depending on the context and location of the methylated cytosines. Generally speaking, DNA methylation can have a repressive effect on gene expression by interfering with the binding of transcription factors or other regulatory proteins to DNA, or by recruiting methyl-binding proteins that can alter chromatin structure and accessibility. For example, DNA methylation at promoter regions, which are sequences near the start of genes that initiate transcription, can inhibit gene activation by preventing the recruitment of transcriptional machinery. DNA methylation can also silence gene expression by targeting enhancers, which are sequences that enhance the activity of promoters from a distance.

However, DNA methylation can also have an activating effect on gene expression in some cases. For instance, DNA methylation at gene bodies, which are sequences that span the coding regions of genes, can facilitate transcriptional elongation and prevent spurious transcription from introns or antisense strands. DNA methylation can also activate gene expression by protecting genes from silencing by other epigenetic mechanisms, such as histone modifications or non-coding RNAs.

In addition to regulating gene expression at specific loci, DNA methylation can also affect genome-wide gene expression patterns by modulating chromatin organization and dynamics. Chromatin is the complex of DNA and histone proteins that forms the structural basis of chromosomes. Chromatin can adopt different states of compaction and accessibility, which can influence gene expression levels and responsiveness. DNA methylation can contribute to chromatin state transitions by interacting with histone modifications and chromatin remodeling factors. For example, DNA methylation can cooperate with histone deacetylation to establish a repressive chromatin state called heterochromatin, which is characterized by high compaction and low gene activity. Conversely, DNA methylation can antagonize histone acetylation to prevent a permissive chromatin state called euchromatin, which is characterized by low compaction and high gene activity.

In summary, DNA methylation is a versatile epigenetic modification that can modulate gene expression in various ways depending on the genomic context and the interplay with other regulatory factors. DNA methylation can have both repressive and activating effects on gene expression at specific loci or across the genome by influencing chromatin structure and dynamics. By doing so, DNA methylation can shape the transcriptional landscape of cells and tissues and mediate their responses to developmental and environmental cues.

DNA methylation was discovered in mammals as early as DNA was identified as the genetic material. In 1948, Rollin Hotchkiss first detected a modified cytosine in the preparation of calf thymus using paper chromatography. He proposed that this fraction was 5-methylcytosine (5mC), a methylated form of cytosine that occurs in DNA. He also suggested that this modification might have biological significance, but the exact role of DNA methylation remained unclear for decades.

In the 1960s and 1970s, several studies revealed that DNA methylation patterns vary among different tissues and cell types, and that they are inherited through cell division. It was also observed that DNA methylation occurs predominantly in CpG dinucleotides, which are regions of DNA where a cytosine is followed by a guanine. However, the function of DNA methylation in gene regulation was still controversial, and some researchers even doubted its existence.

In the 1980s, the advent of molecular cloning and genomic sequencing techniques enabled more detailed analysis of DNA methylation and its effects on gene expression. It was demonstrated that DNA methylation can silence genes by preventing the binding of transcription factors or by recruiting repressive chromatin modifiers. It was also shown that DNA methylation is involved in important developmental processes such as genomic imprinting, X-chromosome inactivation, and embryonic differentiation.

In the 1990s and 2000s, the field of DNA methylation research expanded rapidly with the discovery of new enzymes and mechanisms involved in the establishment and maintenance of DNA methylation patterns. It was also recognized that DNA methylation can be dynamically regulated by various environmental and physiological factors, and that aberrant DNA methylation can contribute to diseases such as cancer. Furthermore, new technologies such as bisulfite sequencing and microarrays enabled genome-wide analysis of DNA methylation profiles in different cells and tissues.

In the 2010s and beyond, the field of DNA methylation research continues to evolve with the development of novel methods and tools for studying the function and regulation of DNA methylation. It is now possible to manipulate DNA methylation in specific genes or regions using genome editing techniques such as CRISPR-Cas9. It is also possible to measure DNA methylation at single-cell resolution using single-cell sequencing or imaging methods. These advances have opened new avenues for understanding the role of DNA methylation in health and disease.

DNA methylation is a type of chemical modification that occurs on the DNA molecule. It involves the transfer of a methyl group (-CH3) from a donor molecule, such as S-adenosylmethionine (SAM), to a specific position on the DNA base. The most common form of DNA methylation in mammals is the methylation of the 5-carbon atom of cytosine (C) within a CpG dinucleotide, resulting in 5-methylcytosine (5mC). CpG dinucleotides are regions where a cytosine is followed by a guanine on the same DNA strand. These regions are often clustered in CpG islands, which are short stretches of DNA with a high frequency of CpG sites. CpG islands are usually located near gene promoters and other regulatory elements.

The process of DNA methylation is catalyzed by a family of enzymes called DNA methyltransferases (DNMTs). There are three main types of DNMTs in mammals: DNMT1, DNMT3a, and DNMT3b. DNMT1 is responsible for maintaining the existing methylation patterns during DNA replication, while DNMT3a and DNMT3b are responsible for establishing new methylation patterns during development and differentiation. DNMTs recognize hemimethylated DNA, where one strand is methylated and the other is not, and copy the methylation pattern to the newly synthesized strand. This ensures that the methylation status of each CpG site is inherited by the daughter cells.

The effect of DNA methylation on gene expression depends on the context and location of the methylated CpG sites. In general, DNA methylation in gene promoters and enhancers tends to repress gene expression by preventing the binding of transcription factors and other regulatory proteins. DNA methylation can also recruit methyl-CpG-binding proteins (MBPs), which can further inhibit transcription by recruiting histone deacetylases (HDACs) and other chromatin-modifying enzymes. These enzymes can alter the histone marks and chromatin structure around the methylated DNA, making it less accessible to the transcription machinery. On the other hand, DNA methylation in gene bodies and introns can have positive effects on gene expression by facilitating transcription elongation and splicing.

DNA methylation is not a static process, but rather a dynamic one that can be influenced by various factors, such as environmental stimuli, cellular signals, and developmental cues. The balance between methylation and demethylation is crucial for maintaining the proper gene expression patterns and cellular functions. Demethylation can occur either passively or actively. Passive demethylation happens when DNMTs fail to maintain the methylation patterns during DNA replication, leading to a gradual loss of methylation over time. Active demethylation happens when specific enzymes remove the methyl groups from the DNA bases, restoring their original state. The main enzymes involved in active demethylation are ten-eleven translocation (TET) proteins, which can oxidize 5mC to 5-hydroxymethylcytosine (5hmC) and other intermediates that can be further processed by base excision repair (BER) enzymes.

DNA methylation is a fundamental epigenetic mechanism that regulates gene expression and cellular identity in mammals. It is essential for normal development and differentiation, as well as for various physiological and pathological processes. Abnormal DNA methylation patterns can lead to diseases such as cancer, neurological disorders, and imprinting disorders.

DNA methylation is not only a mechanism of gene regulation, but also a crucial determinant of cell fate and identity. During mammalian development, DNA methylation patterns are dynamically established and erased in a stage- and tissue-specific manner, resulting in the formation of distinct cell types and tissues with different functions and characteristics. DNA methylation is essential for normal development, as it plays a key role in several processes, such as:

• Genomic imprinting: the differential expression of genes depending on their parental origin . This phenomenon ensures the proper dosage and balance of growth factors and hormones during embryonic and postnatal growth.
• X-chromosome inactivation: the silencing of one of the two X chromosomes in female mammals to achieve dosage compensation with males . This process involves the coating of the inactive X chromosome by a long non-coding RNA called XIST, which recruits DNA methyltransferases and other chromatin modifiers to establish and maintain the repressive state.
• Transposable element repression: the suppression of the transcription and transposition of repetitive DNA sequences that constitute about half of the mammalian genome. These sequences can cause genomic instability and mutations if left unchecked, and DNA methylation is one of the main mechanisms to prevent their activation.

However, DNA methylation is not only important for normal development, but also for disease prevention and progression. Aberrant DNA methylation patterns have been associated with various human diseases, especially cancer . Some examples of how DNA methylation can contribute to disease are:

• Loss of imprinting: the disruption of the parent-specific expression of imprinted genes, which can lead to overexpression or underexpression of growth-related genes. This can result in developmental disorders, such as Beckwith-Wiedemann syndrome and Prader-Willi syndrome, or increased susceptibility to cancer, such as Wilms tumor and colorectal cancer.
• Global hypomethylation: the reduction of the overall level of DNA methylation in the genome, which can affect chromosomal stability, gene expression and transposable element activity. This phenomenon is commonly observed in cancer cells and is associated with genomic instability, aneuploidy and increased mutation rate.
• Gene-specific hypermethylation: the increase of DNA methylation at specific gene promoters or enhancers, which can lead to silencing of tumor suppressor genes or genes involved in DNA repair, apoptosis, cell cycle regulation and differentiation. This phenomenon is also frequently observed in cancer cells and is associated with tumor initiation, progression and resistance to therapy.

Therefore, DNA methylation is a vital epigenetic mark that influences gene expression and cellular function in both physiological and pathological conditions. Understanding the mechanisms and functions of DNA methylation and its interplay with other epigenetic factors is essential for unraveling the complexity of mammalian development and disease.

DNA methylation is a dynamic and reversible process that is regulated by a family of enzymes called DNA methyltransferases (DNMTs). These enzymes catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the 5-carbon of cytosine residues in DNA, resulting in 5-methylcytosine (5-mC).

There are five known DNMTs in mammals: DNMT1, DNMT2, DNMT3a, DNMT3b, and DNMT3L. Among them, DNMT1, DNMT3a, and DNMT3b are the main enzymes responsible for the establishment and maintenance of DNA methylation patterns in the genome.

DNMT1 is the most abundant and ubiquitous DNMT in mammalian cells. It has a strong preference for hemimethylated DNA, which is generated after DNA replication. Therefore, DNMT1 is considered as the maintenance methyltransferase that copies the methylation pattern from the parent strand to the daughter strand during cell division.

DNMT3a and DNMT3b are de novo methyltransferases that can methylate unmethylated DNA. They are essential for the establishment of genomic methylation patterns during embryonic development. They also play a role in tissue-specific and temporal regulation of gene expression by modifying CpG islands and other regions of the genome.

DNMT2 and DNMT3L are two additional members of the DNMT family that have more specialized but related functions. DNMT2 has a weak DNA methyltransferase activity but a strong RNA methyltransferase activity. It mainly methylates transfer RNA (tRNA) and small nuclear RNA (snRNA) and may be involved in regulating protein synthesis and RNA processing. DNMT3L is a catalytically inactive protein that interacts with DNMT3a and DNMT3b and stimulates their activity. It is required for the methylation of imprinted genes and retrotransposons in germ cells.

The activity and expression of DNMTs are regulated by various factors, such as DNA sequence, chromatin structure, transcription factors, non-coding RNAs, post-translational modifications, and environmental stimuli. Dysregulation of DNMTs can lead to aberrant DNA methylation patterns and contribute to various diseases, such as cancer, neurological disorders, and autoimmune diseases. Therefore, understanding the mechanisms and functions of DNMTs is crucial for elucidating the role of DNA methylation in health and disease.

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