Histone Modification and Epigenetics: Deciphering the Biological Significance of Histone Modification

In the realm of epigenetics, histone modification constitutes a crucial research area. It involves a series of chemical alterations to histones subsequent to translation. These modifications do not modify the DNA sequence but exert a substantial impact on gene expression and chromatin structure.

Introduction of Histone Modification

Histone modification refers to the chemical modification of histones (such as core histones H2A, H2B, H3 and H4) on lysine, arginine and other residues, including methylation, acetylation, phosphorylation and ubiquitination. These modifications are usually catalyzed by specific enzymes, such as histone acetyltransferase (HATs) for acetylation, histone deacetylase (HDACs) for deacetylation and methyltransferase for methylation. In addition, histone modification is dynamic and can be added or removed through the action of enzymes, thus realizing the regulation of gene expression.

Histone modifications regulated by the JAK-STAT pathway (Liu et al., 2016)

Histone modification is one of the core mechanisms of epigenetics, which affects the structure of chromatin and the expression of genes by changing the intensity of interaction between histone and DNA. It can change the loose or condensed state of chromatin. For example, lysine acetylation is usually related to the open chromatin structure, which promotes gene transcription, while lysine methylation may be related to the silent chromatin structure.

Histone modification directly regulates gene expression by affecting the binding ability between transcription factors and gene promoters. For example, acetylation usually activates gene expression, while deacetylation may inhibit gene expression. In addition, histone modification can further change the three-dimensional structure of chromatin by recruiting chromatin remodeling complexes, thus affecting the accessibility and expression of genes.

A model of genome organization and epigenetic modifications in V.dahliae (Kramer et al., 2023)

Histone modification plays an important role in gene regulation, mainly in the following aspects. The disorder of histone modification is closely related to the occurrence of many diseases. For example, in cancer, abnormal histone modification may lead to gene expression disorder, thus promoting the occurrence and development of tumors; In diabetes mellitus, the changes of histone modification may affect the expression of insulin-related genes. Because histone modification is reversible and its regulatory mechanism is clear, its related enzymes have become potential drug targets. For example, HDAC inhibitors have been used to treat certain cancers and neurodegenerative diseases.

Main Histone Modification Types

Common histone modifications include acetylation, methylation, phosphorylation and ubiquitination, which play an important role in gene expression regulation, chromatin structural remodeling and cell function.

• Acetylization: It is a well-studied histone modification that is catalyzed by HATs and reversed by HDACs. It plays a crucial role in regulating chromatin tightness and gene transcription. Different acetylation sites on histones have distinct functions. H3K9 acetylation has been implicated in processes related to DNA replication fork damage, while H3K18 acetylation is involved in regulating RNA polymerase III – dependent transcription. Acetylation can also recruit specific protein complexes. These complexes can either activate or inhibit gene expression, depending on the context and the specific proteins recruited. In cancer research, abnormal acetylation patterns have been observed in breast, prostate, and colorectal cancers. Specific hyperacetylated or hypoacetylated chromatin regions have been identified, and these alterations may contribute to tumor development and progression.

Hypermethylated/hypomethylated and hyperacetylated/hypoacetylated chromatin with specific patterns detected in breast cancer, prostate cancer, and colorectal cancer (Samec et al., 2019)

• Methylate: Histone methylation predominantly occurs on lysine residues and can exist in different states: monomethylation, dimethylation, and trimethylation. The impact of methylation on gene expression is highly dependent on the modification site and the cell type. For example, the trimethylation of H3K27 is generally associated with gene silencing. This modification is involved in processes such as X – chromosome inactivation and transcriptional repression. In contrast, H3K4 methylation is typically linked to gene activation. Aberrant H3K27 methylation, such as an abnormal increase in H3K27me3, can lead to the silencing of tumor – suppressor genes, which is a common event in cancer development. Methylation at H3K36 (H3K36me3), which promotes gene transcription, is also significant. Its abnormal expression has been associated with the progression of various tumors, including pancreatic cancer, lung cancer, and acute leukemia.
• Phosphorylation: Histone phosphorylation occurs on serine or threonine residues of histones. It is a key modification for regulating chromatin structure and gene expression. For example, phosphorylation of H3K28 can modulate the activity of RNA polymerase III, which in turn affects gene expression. Phosphorylation is also involved in other critical cellular processes, such as cell cycle regulation, DNA repair, and chromatin remodeling. During the cell cycle, specific histone phosphorylation events occur at different stages to ensure proper chromosome segregation and gene regulation. In DNA repair, phosphorylation can recruit repair proteins to damaged DNA sites, facilitating the repair process.
• Ubiquitination: Histone ubiquitination involves the attachment of ubiquitin molecules to histones. While ubiquitination is commonly associated with the protein degradation pathway, in the context of chromatin, it has distinct functions. It participates in X – chromosome inactivation and histone methylation by recruiting nucleosomes into chromatin. Ubiquitination can also interact with other histone modifications, such as acetylation and phosphorylation, to further regulate gene expression. For example, the interplay between ubiquitination and acetylation can fine – tune the transcriptional activity of genes. In some cases, ubiquitination can enhance the recruitment of transcriptional activators, while in others, it can lead to the recruitment of repressive complexes.
• Other modification: In addition to the major modifications mentioned above, histones can undergo glycosylation, ADP – ribosylation, and other less – characterized modifications. These modifications, although less well – understood, contribute to the complexity of the histone modification network. They work in concert with the more common modifications to precisely regulate gene expression and chromatin structure. For example, glycosylation may affect the interaction between histones and DNA, or between histones and other chromatin – associated proteins, potentially influencing gene accessibility and expression.

Epigenetics regulate the gene expression without alteration in DNA sequence (Qin et al., 2019)

Histone modification has a profound impact on biological processes such as gene expression, cell differentiation and DNA repair by changing chromatin structure, recruiting specific protein complexes and interacting with other epigenetic mechanisms.

To study histone modifications and their role in gene regulation, several sequencing techniques are commonly used. ChIP-Seq (Chromatin Immunoprecipitation Sequencing) allows for the identification of specific histone modifications across the genome by immunoprecipitating modified histones followed by sequencing. MNase-Seq and ATAC-Seq help analyze chromatin accessibility and nucleosome positioning, indirectly reflecting histone modifications’ influence on chromatin structure. HiChIP-Seq combines ChIP-Seq with chromosome conformation capture to study chromatin interactions and histone modifications. Additionally, integrating RNA-Seq with ChIP-Seq enables the exploration of how histone modifications influence gene expression. These techniques are crucial for understanding epigenetic regulation in processes like gene activation, DNA repair, and cancer progression.

If you would like to learn more details, you can check out the following articles:

• ChIP-seq vs. ATAC-seq
• Comprehensive Overview of Chip-seq
• ChIP-Seq: A Versatile Tool for Epigenomics
• Epigenetic Modification: Types, Functions, and Applications in Disease and Development

Relationship Between Histone Modification and Diseases

The role of histone modification in diseases is a complex and important research field, involving the pathogenesis and treatment strategies of cancer, neurodegenerative diseases and many other diseases. The function and clinical application of histone modification are described in detail from three aspects:

The role of histone modification in cancer

Histone modification is a crucial factor in cancer development. Abnormal histone methylation, in particular, is closely linked to the pathogenesis of many cancers. For example, the methylation of histone H3 lysine 27 (H3K27me3) is an inhibitory modification that is often associated with the silencing of tumor – suppressor genes. Demethylases such as UTX and JMJD3, which can remove H3K27me3 and activate gene expression, are frequently mutated or have reduced expression in various tumors. This leads to the sustained silencing of tumor – suppressor genes, allowing cancer cells to evade growth control mechanisms.

Methylation of histone H3K36 (H3K36me3), which promotes gene transcription, is also important in cancer. Its abnormal expression, along with that of its methyltransferase (such as EZH2), can act as a tumor driver. In pancreatic cancer, lung cancer, and acute leukemia, abnormal levels of H3K36me3 have been observed, contributing to uncontrolled cell proliferation and tumor progression. Mutations in histone – modifying enzymes, such as EZH2 overexpression or MLL2 inactivation, are strongly associated with the development of hematological tumors.

Pharmacological restoration of the epigenetic balance of gene expression in human cancers (Zhao et al., 2019)

In clinical applications, targeted therapies against histone modifications have shown promise. HDAC inhibitors and EZH2 inhibitors have been used to treat hematological malignancies. These drugs work by regulating histone modification patterns, restoring the expression of tumor – suppressor genes, and inhibiting tumor growth. For example, HDAC inhibitors can increase the acetylation levels of histones, which may re – activate silenced tumor – suppressor genes, leading to the inhibition of cancer cell growth.

Association between histone modification and neurodegenerative diseases

The role of histone modification in neurodegenerative diseases is mainly reflected in its influence on gene expression regulation. Studies have shown that histone acetylation and deacetylation play an important role in Alzheimer’s disease (AD), Parkinson’s disease (PD) and Huntington’s disease (HD). For example, histone deacetylase (HDACs) inhibitors can reduce neuronal apoptosis and enhance memory and synaptic plasticity in a mouse model of Alzheimer’s disease. In addition, HDAC inhibitors have also been found to improve the motor deficit of Huntington’s disease mouse model.

The changes of histone acetylation level are also closely related to neurodegenerative diseases. For example, in the brain of patients with Alzheimer’s disease, the acetylation level of histones H3 and H4 decreased, while in the brain of patients with Parkinson’s disease, the acetylation level of α -synuclein gene increased. The abnormality of these modifications may promote the progress of the disease by affecting gene expression and neuron function.

The role of acetylation and deacetylation on microtubule stability (Kabir et al., 2022)

At the mechanism level, histone modification regulates gene expression by changing the interaction between DNA and transcription machinery. For example, histone acetylation enhances gene transcription, while deacetylation inhibits gene expression. In addition, histone modification is closely related to the core pathological mechanisms of neurodegenerative diseases such as neuroinflammation, oxidative stress and chronic inflammation.

The application of histone modification in clinical research

In clinical research, the application of histone modification mainly focuses on the diagnosis, treatment and prognosis evaluation of diseases. For example, the mutation of histone modifying enzyme has been used in the diagnosis of genetic diseases. In addition, the changes of histone modification status are also used as biomarkers of cancer and neurodegenerative diseases. For example, abnormal levels of DNA methylation and histone modification can be used as early diagnostic markers of cancer and neurodegenerative diseases.

In terms of treatment, targeted drugs for histone modification have shown potential. For example, HDAC inhibitors not only show curative effect in cancer treatment, but also show protective effect in neurodegenerative diseases. In addition, small molecule inhibitors of histone modifying enzymes have also been developed as potential therapeutic drugs.

Epigenetic regulation of DNA methylation, histone acetylation, and histone methylation (Cheng et al., 2019)

Histone modification plays an important role in cancer and neurodegenerative diseases. Histone modification affects the occurrence and development of diseases by regulating gene expression and chromatin state. In clinical research, the application of histone modification provides a new idea for the diagnosis, treatment and prognosis evaluation of diseases. Future research needs to further explore the specific mechanism of histone modification and develop more effective targeted therapy strategies to improve the prognosis of patients.

Detection Method of Histone Modification

The detection method and research progress of histone modification is a highly complex and rapidly developing field, involving a variety of technologies and methods.

• Chromatin immunoprecipitation (ChIP) technique: ChIP is a classic method to detect histone modification. By fixing the binding of protein and DNA, the unmodified part of DNA is removed, thus the specific modified histone is separated. ChIP can be divided into in-situ ChIP (ChIP-in-place) and cross-linked ChIP (ChIP-on-chip). The former is used to analyze the histone modification in chromatin, and the latter is used to analyze the distribution of histone modification by Qualcomm quantity.
• Mass spectrometry (MS): MS is an important tool for quantitative analysis of histone modification, which can provide high-precision quantitative information of modification sites and types. Common methods include substrate labeling based on enzymatic or chemical catalysis (such as SILAC), unlabeled method (such as PTMScan) and quantitative analysis using stable isotope labeling.

Flowchart showing the characterization of histone PTMs through chemical derivatization and stable isotope peptide labeling (Plazas-Mayorca et al., 2009)

• Surface enhanced Raman scattering (SERS) technique: SERS is a new biological sensing method, which uses gold nanoparticles as the substrate and combines Raman scattering signals to realize high-sensitivity detection of histone modification. This method is rapid and simple without antibody labeling.
• Multiple magnetic bead array: Using magnetic bead array technology, many histone modifications can be detected simultaneously. For example, multiple magnetic bead array can detect various post-translational modifications (PTMs) of histone H3, and combine it with Qualcomm analysis platform for data processing.
• In situ proximity detection (in situ PLA): PLA technology detects the coexistence of histone modifications through antibody-mediated double probe binding. This method is suitable for analyzing histone modifications in heterogeneous cell populations and tissue sections.

Research Progress and Clinical Application of Histone Modification

Histone modification has great potential in clinic. It can be used as a marker of disease diagnosis and realize early and accurate diagnosis. In the treatment, drugs targeting histone modifying enzymes have been used in cancer, and future combined therapy may be synergistic. In regenerative medicine, it can regulate cells and help tissue repair. In addition, personalized medical care can be developed based on individual modification characteristics.

Relationship between histone modification and diseases

Histone modification plays an important role in the occurrence and development of many diseases.

• Tumors: Abnormal histone modification is an important driving factor for tumorigenesis. Studies have shown that histone methylation and acetylation are closely related to the occurrence and development of tumors, and can be used as potential targets for tumor diagnosis and treatment.
• Metabolic diseases: The abnormal increase of histone acetylation level of peripheral blood mononuclear cells in patients with type 2 diabetes suggests that histone modification may be involved in the occurrence of metabolic diseases.
• Cardiovascular diseases: Abnormal histone modification is closely related to the occurrence and development of cardiovascular diseases such as atherosclerosis and congenital heart disease.

Regulation mechanism of histone modification

Histone modification is catalyzed by many enzymes, including methyltransferase, acetyltransferase and deacetylase. The activity regulation of these enzymes is the key to the dynamic change of histone modification. For example, HDAC inhibitors and EZH2 inhibitors have been used in the clinical treatment of some hematological tumors.

Reversibility and therapeutic potential of histone modification

Histone modification is reversible and can be reversed by demethylase or deacetylase. This characteristic provides a new idea for the treatment of diseases. For example, histone modifying enzyme inhibitors for liver cancer can reverse the abnormal modification pattern of cancer cells, thus achieving therapeutic effects.

Application of histone modification in precision medicine

Histone modification is an important part of epigenetics, and its abnormal pattern can be used as a biomarker of diseases. By detecting the changes of specific histone modification sites, early diagnosis and individualized treatment of diseases can be realized.

There are various detection methods of histone modification, including ChIP, MS, Raman scattering biosensor and so on, each with its own advantages and disadvantages. In recent years, with the progress of technology, the research on histone modification has made remarkable progress, revealing its important role in the occurrence and development of diseases. In the future, the study of histone modification will further promote the development of precision medicine and provide a new direction for the diagnosis, treatment and prognosis of diseases.

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