What is gene expression analysis?
Gene expression is the process of using information encoded in genes to synthesize a functional gene product. Since genes are transcribed into RNA, which is either translated into protein or serves as a functional RNA end product [e.g., non-coding RNAs
(ncRNAs) and long, non-coding RNAs (lncRNAs)], RNA transcript levels are generally equated to a measure of expression of the gene. Thus, gene expression analysis typically quantifies either messenger RNA (mRNA) levels as the first step towards protein
expression, or quantifies non-translated, functional RNA.
Why measure gene expression?
Linking the expression of specific genes to a biological process or phenotype helps scientists understand gene function, biological pathways, and the genes that regulate development, cell behavior, cell signaling, and disease. The specific gene expression
patterns or “gene signatures” associated with a biological state can serve as biomarkers for that condition, and, in the example of disease, can be used in identification, diagnosis, and assessment of treatment success. Similarly, determining
changes in gene activity resulting from specific environmental and physical factors can reveal the effect of these factors. Such evaluation helps medical professionals understand the impact of medications and facilitates research towards developing
more effective drugs. Likewise, this analysis can identify conditions under which specific crops are induced to thrive.
How is gene expression measured?
Measuring gene expression has traditionally involved isolating an intact RNA fraction from samples, immobilizing it, and detecting and quantifying the RNA transcripts of interest. This is usually done using a transcript-specific, labeled probe. Gene expression
techniques that use this approach have been limited by their ability to study only a few transcripts per experiment. These include: northern blotting, dot blotting, ribonuclease protection assays (RPAs), serial analysis of gene expression (SAGE),
and differential or subtractive hybridization.
Current approaches provide greater detection efficiency and allow for increased target and sample number. They usually involve adding multiple probes to an RNA fraction or directly to a cell lysate. These include quantitative PCR (qPCR), digital PCR (dPCR),
next generation sequencing (NGS), microarrays and panels, and in situ hybridization, including fluorescent in situ hybridization (FISH).