A genome is the genetic material present within an organism. This information is, specifically, present within the Deoxyribonucleic Acid (DNA), for all organisms, and the ribonucleic acid (RNA), for some viruses. The DNA is a double-stranded helix that consists of 4 building blocks called nucleotides; these are adenine (A), guanine (G), cytosine (C) and thymine (T). Since the DNA consists of two strands, these building blocks are paired to each other in the opposite strand, where the A always pairs with the T and the C pairs with the G.
Another feature of the DNA is that it consists of coding regions and non-coding regions; coding regions are the sequences that are later translated into protein structures, while non-coding regions are not translated. However, this does not mean that non-coding regions are useless, as was assumed several years ago. These sequences play a crucial role in the regulation of processes such as transcription and translation, which are processes required for the coding sequences to be transformed into proteins.
With that being said, Genomic analysis consists of a set of tools that are crucial for the identification and measurement of important features within the DNA sequence; these consist of a variety, ranging from structural differences/similarities to regulatory elements that play a role at the genetic level. In this article, we will introduce the different methods of genomic analysis and the importance of these types of analyses in our everyday life. To study the genome of an individual, we first need to determine the different ways/fields one can analyze a genome. There are four main ways: structural, functional, comparative and mutational:
During the structural analysis of the genome, the physical natures of its components are identified. During this step, the 3D structure of a protein, formed from a specific sequence, is determined. This can help us define the function of a protein, especially if a similar structure is observed in another species. Tools, such as X-ray crystallography and protein modeling, within the field of biochemistry and bioinformatics, can help us with this analysis. This is usually observed in the drug design process, where people try to find or synthesize drugs that have similar structures to the target protein.
One main issue with structural genomics is that not all similar structures have identical functions. Furthermore, certain coding genes have unknown functions and are unrelated to other genes. On the other hand, functional genomics involves the determination of the biological function of a gene, which may allow us to identify the biochemical pathway this gene plays a role in. This method of analysis comprises fields such as transcriptomics, proteomics, and bioinformatics. Several tools are utilized in this field, such as next-generation sequencing and DNA and protein microarrays. This area of study has been gaining traction in the scientific field due to its complexity and the vast amount of data that can be obtained since one gene can produce several products. To aid in simplifying the analysis process, the experts at Onramp.bio recommend researching the necessary tools or facilities that may have them readily available. The importance of functional genomics can be observed in medicine, where scientists diagnose diseases within patients by determining markers based on the upregulation or downregulation of certain genes during the diseased state as compared to the healthy state.
As the name suggests, mutational genomics is the study of mutations connected to genes. This is mainly observed in cancer, in the field of oncogenomics, where changes in the nucleotides result in either the upregulation or downregulation of certain gene products. This, in turn, leads to an abnormally functioning system. This, similar to functional genomic, may lead to the identification of markers, that might result in better diagnosis, prognosis, and therapeutics. To study these mutations, one may introduce them deliberately, targeting a certain gene, or indiscriminately.
Comparative genomics involves the comparison of different genomes from different species. The purpose of this process is to determine certain evolutionary aspects. In other words, by looking at the genomes of different organisms and comparing them with one another, we can determine molecular and biochemical processes that distinguish different organisms. Furthermore, we can identify, across species, the conserved or common DNA regions; this would shed light on the extreme importance of such sections. Another important aspect of comparative genomics is its ability in determining the evolutionary origin of a species. Usually, computational tools are utilized for such studies.
Ultimately, as presented, genomic analysis is a complex field. However, it has contributed significantly to several fields such as virology and genealogy. Furthermore, it utilizes a vast amount of tools within the fields of molecular biology, biochemistry, and bioinformatics. Through these emerging knowledge and tools that help us dig into the human genome, we can expect the cure to many diseases will soon be at hand.