Microarrays – Studying Gene Expression

One of the major areas of Bioinformatics is creating tools to analyze data generated from genome sequencing and other DNA research tools.  It is, therefore, crucial to understand the fundamentals of these procedures.

Imagine you have a sample of cancer cells and a sample of healthy cells, and you would like to investigate the difference in the expression of a particular group of genes between the two of them. DNA microarrays allow you to do just that!

First, we need to collect messenger RNA (mRNA) from both samples. However, this molecule tends to be unstable, so the next step is to generate a DNA sample from the mRNA – using reverse transcription – called complementary DNA (cDNA).

Each sample will be labeled with a fluorescent probe. For example, the cDNA sample from the cancer cells will be labeled with a red fluorescent dye, while the healthy cells will be labeled with a green one. After this marking, we can mix the samples together, and place them on a solid support called the microarray slide, which has tiny spots.

Each one of these spots has a known DNA sequence, the probe. By placing our sample in each spot, hybridization will occur, which is the process of joining two complementary strands of nucleic acids – RNA, DNA or oligonucleotides.

Notice that it’s necessary to know the DNA sequence of the genes that are to be studied in advance so that we can make our probes.

We can quantitative deduce the gene expression of each sample by observing the final color of each spot. For example, a spot displaying a bright red color means that there was more cDNA from the cancer cell sample to bind to the DNA probe, which in turn means that the expression of the gene is superior in this sample, rather than in the healthy cell sample (greater expression of the gene implies a greater quantity of mRNA, leading to a greater quantity of cDNA). If the expression is higher in the healthy cell sample, the spot turns green. And if it’s a tie? Well, in that case, the dot will have a yellowish color!

Microarray - red: cDNA hybridization of the test sample; green: cDNA hybridization of the control sample; yellow: hybridization of both samples; black: no hybridization.By Paphrag at English Wikipedia (Transferred from en.wikipedia to Commons.) [Public domain], via Wikimedia Commons
Microarray – red: cDNA hybridization of the test sample; green: cDNA hybridization of the control sample; yellow: hybridization of both samples; black: no hybridization. By Paphrag at English Wikipedia (Transferred from en.wikipedia to Commons.) [Public domain], via Wikimedia Commons

If you’d like to know more about how this technique applies in Microbiology, check out this article :
“This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.”

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