Exploring “Omics”: a review of Genomics and Metabolomics

Last update: July 30, 2016

Overview: what is “Omics”?

The term “Omics” is an English language Neologism which is utilized to informally refer to the totality of any biological field of study. Using the suffix “–ome”, new areas of study have been demarcated such as genome, proteome or metabolome, while new ones are constantly being added on a regular basis (transcriptome, interactome, proteome etc…). What this essentially does is that it allows the researchers to significantly broaden the scope of and the means of their study, because multi-omics approaches allow the comparison of complete biological systems to better understand how their intersection and interaction affects the organism as a whole.

Genomics

One of the more popular “omics”, Genomics is an offshoot of Genetics that deals in the application of DNA sequencing and bioinformatics to sequence, assemble, and analyze the function and structure of entire genomes. The comprehensive nature of this field means that it usually deals with complete DNA sets rather than studies of single genes, unless the purpose of the study is to understand and analyze the interaction and the effects of the individual gene on the larger network. Genomics in turn can be classified into multiple subsets of research areas which include:

Functional Genomics

This particular area of study aims to utilize the comprehensive datasets and use this information to understand as well as describe gene and cell functions. The focus of this area of study is the dynamic aspect of biological functions such as the ongoing processes of gene transcription and translation and protein synthesis and interaction, not more static permanent aspects such as gene sequencing.

Structural Genomics

Structural genomics encompasses the study of the 3-dimenstional nature of protein structures as encoded by a given genome. In this sense structural genomics can be used as a synonym for proteomics. The focus of the study is to determine the 3-D structure of every protein synthesized using the encoding by particular genes instead of focusing on a single protein. The availability of complete gene sequences further speeds up the process of structure prediction with the utilization of a combination of experimental and modeling approaches.

Epigenomics

Another area of research within Genomics is known as Epigenomics. This deals with the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. Epigenetic modifications are changes to the DNA structure or histones of cells, which while being reversible in nature, affect gene expression without altering the physical gene structure and sequence. This area of research is also relatively new and made possible through the adaptation of genomic high-throughput assays.

Taking into consideration the variation in the genome, transcriptome, proteome and metabolome and the manner in which they interact with each other and environment, every individual has a unique makeup with regards to biology. This is why the utilizing “multi-omics” in research is fast gaining popularity in the scientific community and is considered as an effective way of understanding biological systems.

Another “Ome” that compliments the study of Genomes is Metabolome.

Metabolomics

The scope of Metabolomics is the identification of any small molecule produced as intermediate or end product in any chemical process taking place within the human body. Some authors separate the study of the chemical processes involving endogenous human molecules (Endogenous Metabolome) from the study of processes involving external molecules introduced into the body (Exogenous Metabolome).

The key feature of metabolomics is that metabolites are closely linked to the phenotypes of the organism. A comprehensive record of biochemical activities of the organism is therefore of help in understanding human diseases.

Measuring metabolites

Metabolites are small molecules with a typical molecular weight of <1500 Da and are measured via the utilization of various methods and technologies such as NMR spectroscopy and mass spectrometry. Contingent on the mode of protocol and the nature of instrument, a metabolome analysis can identify up to 100,000 different metabolites and more.

Metabolome databases

The key element controlling the composition of an organism’s metabolome is its genome; because of this, different organisms will have different metabolomes. Additionally, each individual organs and tissues may display characteristically different metabolomes. The complexity of this situation has led to the development of a number of organism-specific or biofluid-specific metabolome databases, which include the Human Metabolome Database or HMDB, the Yeast Metabolome Database or YMDB, the E. Coli Metabolome Database or ECMDB, the Arabidopsis metabolome database or AraCyc as well as the Urine Metabolome Database, the Cerebrospinal Fluid (CSF) Metabolome Database and the Serum Metabolome Database.

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