Array-based Methylation Detection Explores the Mysteries of Cancer

Posted by kiko on August 25th, 2022

Epigenetics is an emerging field of research that focuses on the effects of environmental factors, such as infections, pollutants, stress, and long-term drug exposure, on an individual's genome. Epigenetic changes do not alter the structure of DNA, but do alter the way DNA is modified. Thereby, those changes include DNA methylation, histone modifications and non-coding RNAs. affects gene regulation.

Diseases And Epigenetic Modifications

The occurrence of some diseases has been found to be inextricably linked to epigenetics. Cancer is caused by gene mutations and epigenetic alterations of genes. Among the six possible mechanisms leading to oncogenes with an altered expression that cause cancer, three of them are directly related to DNA methylation and histone acetylation.

One of the Immunodeficiency diseases, ICF syndrome is caused by mutations in the DNA methyltransferase 3b (DNMT3b) gene. Studies have shown that patients with abnormal chromosomes 1, 9 and 16 have a large number of repetitive typical satellite DNA sequences near their mitoses, and these repetitive sequences exhibit hypomethylation.

Epigenetic factors such as DNA methylation, histone modifications, and non-coding RNAs are associated with a variety of diseases such as tumorigenesis, immunodeficiency diseases, neurological disorders, cardiovascular diseases, and psychiatric disorders. However, unlike associated diseases caused by genetic mutations, many epigenetic alterations are reversible, which offers optimistic prospects for disease treatment.


What is A Gene Microarray?

Microarray is also commonly known as gene chip, also known as DNA microarray. The technology fixes high-density designed oligonucleotide or cDNA sequence dot matrix on the chip surface, labeling fluorescent probes for nucleic acid hybridization, and detecting the hybridization signal by laser confocal scanning microscope, to obtain nucleotide sequence information. It has a higher resolution compared with traditional karyotype analysis techniques and can identify subtle chromosomal imbalances above the Kb level.

The principle of gene chips is based on hybridization, i.e., a method of nucleic acid sequence determination by hybridization with a set of probes of known genes, where probes with target nucleotides of known sequence are immobilized on the surface of a substrate.

Microarray Analysis in Methylation Detection

A number of hypomethylation intervals (hypomethylated blocks) are prevalent in multiple cancers. Ninety-five percent of the DNA methylation changes in cancer occur in those regions.  Epigenetics microarrays are products specifically designed to study disease-related block regions. It can detect changes in DNA methylation, histone modifications and transcription factor binding sites.

The microarray can not only focus on cancer-specific regions of large-scale epigenetic changes, but also specifically detect small-scale methylation changes. More than 10,000 cancer-specific DMR regions have been identified, among which the regions of hypermethylated CpG islands are sensitive regions for cancer-related methylation changes. CpG microarrays specialize in differentially methylated regions and can be used to detect methylation changes between samples to study tumor epigenomics from a new perspective.

In addition, in combination with expression profiling microarrays, the regulation of gene expression by epigenetics can be analyzed. The effect of candidates on epigenetic reprogramming can also be validated and studied.

Currently, epigenetic bioinformatics analysis, along with DNA microarray technologies related to DNA methylation, histone modification and chromatin analysis, can be used to study epigenetic processes, helping elucidate epigenetic features and providing a means for disease treatment research, such as the development of methylation inhibitors, deacetylation inhibitors, etc.

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