Introduction
Epigenetic modifications, which involve changes to the genome without altering the DNA sequence, play a crucial role in regulating gene expression. These modifications include chromatin remodeling, DNA methylation, and histone modifications, which are both reversible and heritable. Epigenetic mechanisms provide an additional layer of control within cells, influencing gene expression and silencing, and are essential for processes like cell differentiation (Fardi, Masoumeh, et al., 2018). For example, chemical modifications of histone proteins can lead to either an open euchromatin state, facilitating gene expression by allowing transcription factors and enzymes access to the DNA, or a closed heterochromatin state, which suppresses gene expression by preventing transcription.
This article explores the importance of studying epigenomes, with particular attention to the structure of nucleosomes, chromatin remodeling, and key epigenetic modifications such as DNA methylation, histone tail modification, and non-coding RNA (ncRNA)-associated gene silencing. Additionally, it will examine the implications of epigenetics in cancer, alongside the challenges and prospects in this field.
Epigenomics
Study of the epigenetic modifications at the genome-scale. The epigenome consists of chemical changes that control which genes are turned on or off, playing a critical role in defining cell identity and function during development and differentiation. DNA methylation and histone modifications are the major epigenetic mechanisms that regulate gene expression patterns in cells without altering the DNA sequence. Mediates environment-gene interactions
Why do we study epigenomes?
- Epigenetic modifications greatly impact the gene expression state of a cell.
- Aberrant epigenetic changes are associated with diseases like cancer. Studying epigenomic alterations facilitates development of biomarkers and drug targets.
- Impact of epigenetic modifications on gene expression:
- Methylation of cytosine residue in CpG islands in promoters leads to silencing of gene expression
- Histone modifications: The site of modification determines the activation or silencing of gene expression
- Genome-wide study of epigenetic modifications
- DNA methylation, histone modifications, chromatin remodeling, and 3D genome configurations
- Epigenome plays key roles in the development, differentiation, and diseases
- NGS technologies provide high-throughput approaches that are sensitive and specific.
Structure of nucleosome
The basic repeating unit of chromatin is the nucleosome, typically composed of an octamer of the four core histones H2A, H2B, H3, and H4, and 146 base pairs of DNA wrapped around the histones. Each core histone is composed of a structured domain and an unstructured amino-terminal ‘tail’ of 25-40 residues. ….. Histone tails provide sites for a variety of posttranslational modifications, including acetylation, phosphorylation, and methylation…. such modifications of histone tails determine the interactions of histones with other proteins, which may in turn also regulate chromatin structure. Identifying the multitude of histone modifications, the enzymes that generate them, and the nuclear response to any given pattern of alterations poses a fascinating challenge. (Grant, 2001).
Chromatin remodeling
Change in chromatin structure due to alterations in association with histones, sliding and shifting of histones in the DNA chromatin remodellers e.g, histone acetyltransferases (HATs)
Types of epigenetic modifications
- DNA methylation
- Histone tail modification
- non-coding RNA (ncRNA)-associated gene silencing.
DNA methylation
Methyl groups are added directly to the DNA base on the A or C base. However, it is not limited to methyl groups, could also be hydroxymethyl- or carboxyl groups. Catalyzed by DNA methyltransferase enzymes, DNA methylation involves the addition of a methyl group directly to a cytosine nucleotide within a cytosine-guanine sequence (CpG), which are often surrounded by other CpG’s forming a CpG island. CpG islands are common targets for epigenetic DNA methylation, notably the CpG islands within promoter regions. Indeed, it has been reported that around 70% of gene promotor regions lie within CpG islands (Al Aboud NM, Tupper C, Jialal I. Genetics, Epigenetic Mechanism.)
Methylation on Cytosine base
Methylation on Adenine base
Histone tail modification
Proteins that help in the packing of DNA in the nucleus. DNA wraps around histones methylation, acetylation, etc. of histone residues. Chemical modification of histones affects the binding of histones to DNA. Histone tail modifications are chemical changes to the amino-terminal tails of histone proteins that regulate gene expression.
These modifications include:
- Acetylation: The acetylation and deacetylation of the ε-amino groups of conserved lysine residues present in histone tails …. linked to transcriptional activity and … most intensively studied histone modification. Acetylated histones are usually associated with transcriptionally active chromatin and deacetylated histones with inactive chromatin. (Grant 2001)
- Methylation: A common posttranslational modification that regulates gene expression and transcription.
- Phosphorylation: A post-translational modification that involves adding a phosphate group to specific amino acid residues in the histone tail. This can affect the structure and function of chromatin.
How do we study epigenomes?
1st generation methods (small-scale and localized)
- Sanger sequencing
- PCR amplification-based detection
- restriction enzyme digestion
2nd generation methods (genome-wide)
- microarray-based
3rd generation Current methods (genome-wide, sensitive and specific)
- Next Generation Sequencing (NGS) based
Epigenetics and cancer
Cancers often show marked hypermethylation of tumor suppressor genes and hypomethylation of proto-oncogenes, both of which contribute to tumor carcinogenesis. (Fardi, Masoumeh, et al. 2018). In cervical cancer patients, DNMT1 was expressed in more than 70% of cancer cells, whereas only 16% of normal cells expressed DNMT1 – DNA methyltransferases (Cheng, Yuan, et al. 2019). Several classes of drugs have been developed to target these epigenetic alterations:
- DNA Methyltransferase Inhibitors (DNMTi) – reactivate silenced tumor suppressor genes. Eg, azacitidine and decitabine
- Histone Deacetylase Inhibitors (HDACi)
Challenges and Future Prospects
- Selectivity– Epigenetic events are ubiquitously distributed across normal and cancer cells. – Many current epigenetic drugs lack specificity and can affect normal cells, leading to side effects. Identifying specific biomarkers that predict which patients will benefit from these therapies is crucial for improving outcomes (Cheng, Yuan, et al.)
- Ongoing research is focused on understanding the specific epigenetic alterations associated with different tumor types to develop tailored therapies
Further readings
- Bernstein et al., The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010; 28:1045-8.
- International Human Epigenome Consortium https://ihec-epigenomes.org/
- Cancer genome DNA methylation studies
- TCGA-GDC: https://portal.gdc.cancer.gov/
- ICGC : https://dcc.icgc.org/repositories
References
- Huang C, Wu JC. Epigenetic Modulations of Induced Pluripotent Stem Cells: Novel Therapies and Disease Models. Drug Discov Today Dis Models. 2012;9:e153-e160.
- John RM, Rougeulle C. Developmental Epigenetics: Phenotype and the Flexible Epigenome. Front Cell Dev Biol. 2018;6:130.
- Cantone I, Fisher AG. Epigenetic programming and reprogramming during development. Nat Struct Mol Biol. 2013;20:282-9.
- Hayashi et al. Type-specific roles of histone deacetylase (HDAC) overexpression in ovarian carcinoma: HDAC1 enhances cell proliferation and HDAC3 stimulates cell migration with downregulation of E-cadherin. Int. J. Cancer 127, 1332–1346 (2010).
- Xiao et al., N6-Methyladenine DNA Modification in the Human Genome. Mol Cell. 2018 Jul 19;71(2):306-318.e7.
- Grant, P. A. (2001). A tale of histone modifications. Genome Biology, 2(4), reviews0003.1. https://doi.org/10.1186/gb-2001-2-4-reviews0003
- https://sph.tulane.edu/analysis-histone-modification-osteoporosis-risk
- Al Aboud NM, Tupper C, Jialal I. Genetics, Epigenetic Mechanism. [Updated 2023 Aug 14]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2024 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK532999/