Functional genomics is a branch of genomics that focuses on patterns of gene expression and interaction in the genome. In particular, it is used to measure the expression levels of RNA and proteins to increase understanding of the biological function of the genes of a cell.
The main aim of functional genomics is to utilize the wealth of data produced by genomic and transcriptomic projects to describe the functions and interactions of a genome and phenotype. It looks at the dynamic aspects of the genes, such as transcription, translation, expression, and protein-protein interactions, and aims to explain these processes based on information about the genome.
The results of functional genomics attempt to answer questions about DNA function and behavior. A genome-wide approach is usually taken to study the role of the genes – this is done rather than focusing on each gene separately, which can often be done in traditional genomics studies.
Functional genomics promises to expand the practical knowledge of the effect that an organism’s genome has on its biological function. This could have a significant impact on the way we treat human genetic diseases in the future and has the potential to revolutionize our current health system.
Techniques and applications
There are various techniques or types of analyses that may be performed as a part of functional genomics to investigate the function of certain genetic patterns in the genome. Some of these include:
- Characterization of proteome by ORF: Computer analysis of the DNA sequence searches for segments that begin with the AUG codon, which is the codon that signals for translation to start, until one of the known stop codons is reached. The function of the ORFs can then be studied by the examination of its location, orientation and clustering, which provide important genomic information.
- Gene disruption knockouts: An investigation of ORF function can be performed using in vitro mutagenesis to knock the gene out and observing for a mutant phenotype, which may elude to the function of the ORF.
- Yeast two-hybrid system: This uses the yeast GAL4 transcriptional activator to examine protein interactions throughout the proteome. GAL4 consists of a DNA-binding and an activation domain, which must be on opposite side of the protein if transcription is to occur. In the analysis, the gene is spliced next to the DNA binding domain of the protein to act as “bait”, and another gene is spliced next to the activation domain of another protein as the “target”. Both plasmids are then put into the same cell and this is observed for a physical reaction when the bait and target proteins bind together, causing the GAL4 binding and activation domain to come together.
- Development regulation with DNA chips: This uses samples of DNA that are laid out in patterns on a small glass “chip” to examine regulation of DNA. The technique can help to identify protein networks that are active at a certain stage or sequences of genes.
- Quantitative PCR: This compares the quantity of a specific transcript in two or more RNA isolations. Real time PCR is an alternative type of this technique, involving a fluorescent probe that provides information about the quantity of DNA present.
These techniques can be used to acquire valuable insights about the genome that could be used in practice. We have already completed the Human Genome Project and have a large quantity of data about the genetic basis of human data. However, we lack understanding of how this information can be used to improve human life and health. Function genomics helps to bridge this gap and paves the way for knowledge about genomes to be applied to real life situations in the future.
Reviewed by Afsaneh Khetrapal BSc (Hons)