Epigenetic changes refer to modifications in gene activity that do not involve alterations in the DNA sequence itself. These changes can be either genetic or acquired, and they play a crucial role in regulating gene expression. One of the most common epigenetic mechanisms is DNA methylation, particularly in CpG islands located in promoter regions or the first exon. When these regions become methylated, it often leads to gene silencing. In addition, histone modifications, such as acetylation, also contribute to epigenetic regulation—acetylated histones are typically associated with active gene expression.
Abnormal methylation patterns, especially in CpG islands, can cause both gene silencing and overexpression, which may lead to various diseases, including cancer. However, traditional methods are limited in their ability to analyze methylation on a genome-wide scale. To overcome this challenge, researchers have combined epigenetic analysis with microarray technology, enabling high-throughput and precise methylation profiling.
Two major chip-based methylation analysis techniques have emerged: Methylation-Specific Oligonucleotide Arrays (MSO) and Differential Methylation Hybridization (DMH). The MSO method involves treating DNA with sodium bisulfite, which converts unmethylated cytosines into uracil, while methylated ones remain unchanged. This allows for the detection of specific methylation sites, but it is mainly used for known genes and lacks scalability for large-scale studies.
On the other hand, DMH offers a more comprehensive approach. It uses a CpG island library and isolates methylated DNA fragments using a methyl-CpG binding domain. The process includes digesting genomic DNA with restriction enzymes, enriching for GC-rich fragments, and constructing a library. These fragments are then used to create a microarray for hybridization. The technique has been successfully applied to both nylon membranes and glass chips, significantly increasing throughput and accuracy.
DMH has proven valuable in studying epigenetic changes in breast and ovarian cancers. It has revealed that hypermethylation of CpG islands can silence tumor suppressor genes, contributing to cancer progression. Moreover, different methylation patterns are associated with distinct tumor types and stages, making them potential biomarkers for diagnosis and classification.
Research by Ottaviano et al. confirmed the effectiveness of methylation-specific strategies, while Rober et al. demonstrated the importance of p16 promoter methylation in tumor development. These findings highlight the potential of methylation profiling as a tool for understanding cancer biology.
In conclusion, methylation analysis holds great promise for clinical applications, such as developing new diagnostic tools and therapies targeting DNA methylation or histone deacetylation. As research continues, we can expect even more breakthroughs in the field of epigenetics.
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