Genomics: The outcome of innovations in sequencing technologies led to deciphering of whole genome sequences of different organisms and the branch of omics popularly known as genomics came into existence. The genomics reflects the study of the genome in totality and is further classified into several subbranches as listed below.
Comparative genomics
The major principal underlying comparative genomics is that the common feature between the two organisms is encoded by the conserved DNA sequence. Conversely, divergence between the species is defined by the sequences that encode proteins or ribonucleic acids (RNAs). The comparative genomics provides an insight into the evolutionary aspects of organisms compared based on the sequences at whole genome level. It helps in discriminating conserved sequences from divergent ones. Further, comparative genomics can also be useful to understand the variability in terms of functional DNA segments, such as coding exons, noncoding RNAs, and also some gene regulatory regions. The genome sequences are compared by aligning them to score the match or mismatch between them. Various software and algorithms have been developed for the alignment of several genome sequences simultaneously and elucidate genome evolution and function.
Functional genomics
Functional genomics is applied to test and extend hypotheses that emerge from the analysis of sequence data. Elucidating the functions of identified genes of the sequenced genome of an organism is the sole purpose of functional genomics. While sequencing projects yield preliminary results, functional genomics focuses on the functional aspects such as regulation of gene expression, functions and interaction of different genes, etc. Functional genomics means genome-wide analysis through high-throughput methods. Hence it provides an overview of the biological information encoded by the organism’s genome. The encyclopedia of DNA elements (ENCODE) project is a much-anticipated project, which aims to recognize all the functional elements of genomic DNA both in coding and noncoding regions.
Metagenomics
Metagenomics is emerging as an important discipline to access the biocatalytic potential of unculturable microorganisms. Despite very rich microbial diversity of the range of a million species per 1 g of soil, very few microorganisms can be cultured under in vitro conditions. With the advances made in the field of metagenomics, DNA can be extracted from environmental samples from which genomic library can be prepared. This library can be further explored by screening the clones for biological activity to identify clones possessing desired characteristics. A number of biocatalysts such as laccase, xylanase, endoglucanase, exoglucanase, and lipase have been recently identified from metagenomic libraries.
Epigenomics
Epigenetics refers to the external modification of DNA. It alters the physical structure of DNA without altering the DNA sequence. The DNA methylations, that is, the addition of a methyl group, or a “chemical cap,” to part of the DNA molecule and histone modification are examples of epigenetic changes. Epigenetic changes can be carried over to the following generation if the modifications occur in sperm or egg cells. But most of these epigenetic changes get corrected during reprogramming of fertilized eggs. Cellular differentiation is also an example of epigenetic change in eukaryotic biology. Epigenetic mechanisms are influenced by many other factors such as prenatal development and in childhood, environmental influence, drugs, aging, diet, etc.
Personal genomics
The completion of human genome project has provided valuable information regarding variations of the human genome. Single nucleotide polymorphism (SNP), copy number variation, and complex structural variations can be typed with the help of sequencing data. An ambitious personal genome project (PGP) has been initiated to truly understand the genesis of most complex human traits—from deadly diseases to the talents and other features that makes every individual unique. PGP is widely supported by the nonprofit PersonalGenomes.org, which works to publicize genomic technology and knowledge at a global level. This might be useful for disease management and understanding of human health. It also deals with the ethical, legal, and social issues (ELSI) related to personal genomics.
Cognitive genomics
The brain is an important organ of an organism that helps to deal with the complex, information rich environment. The blueprint for the brain is contained in the genetic material, that is, DNA of an organism. Brain development and cognitive or behavioral variability among individuals is a complicated process that results from genetic attribute of the person as well as their interactions with the environment. In cognitive genomics, cognitive function of the genes and also the noncoding sequences of an organism’s genome related to health and activity of the brain are being studied. Genomic locations, allele frequencies, and precise DNA variations are analyzed in cognitive genomics. Cognitive genomics have immense potential for investigating the genetic reasons for neurodegenerative and mental disorders such as Down syndrome, Autism, and Alzheimer’s disease.
Transcriptomics
Till date several genome sequencing projects have been completed and efforts are now being made to decipher the functional roles of different identified genes, their role in different cellular processes, genes regulation, genes and gene product interaction, and expression level of genes in various cell types. Transcription being the primary step in gene regulation processes, the information about the transcript levels is a prerequisite for understanding gene regulatory networks. The functional elucidation of the identified genes in totality is a subject matter of transcriptomics. It deals with the study of the complete set of RNAs/transcriptomes encoded by the genome of a cell or organism at a specific time and under a specific set of conditions. The techniques that are frequently used for genome-wide analysis for gene expression are complementary DNA (cDNA) microarrays and protein microarrays, cDNA–amplified fragment length polymorphism (AFLP), and serial analysis of gene expression (SAGE).
Proteomics
Proteomics is a comprehensive study of proteins in totality identified in a cell, organ, or organism at a particular time. The complexity of diverse physiological processes and biological structures hinders the applicability of proteomics, though the advent of recent proteomic techniques enables large-scale, high-throughput analyses, identification, and functional study of the proteome. For convenience, the proteomics can further be studied in different subbranches such as structural genomics, immunoproteomics, proteogenomics, nutriproteomics, etc.
Structural genomics
It aims to decipher the 3D structure of all proteins encoded by a particular genome using either experimental tools or in silico tools or sometimes both. In structural genomics, the structure of the total number of identified protein of particular genome is determined while in traditional structural prediction, structure of only one particular protein is determined. Through the availability of full genome sequences of number of organisms, structural prediction can be done by using both the experimental and modeling approaches, as well as previously known protein structures. The sequence-structure–function relationship provides an opportunity to analyze the putative functions of the identified proteins of an organism under purview of structural genomics.
Immunoproteomics
Immunoproteomics is the study of proteins solely associated with immune response with the aid of diverse techniques and approaches. Immunoproteomics encompasses a rapidly growing collection of techniques for identifying and measuring antigenic peptides or proteins. The approaches include gel- and array-based, mass spectrometry, DNA-, and bioinformatics-based techniques. Immunoproteomics is purposely used for understanding of disease, its progression, vaccine preparation, and biomarkers.
Proteogenomics
Proteogenomics is the study that uses proteomic information, mainly derived from mass spectrometry, to improve gene annotations. It is a field of junction of the genomics and proteomics. Previously, the genomics and proteomics studies were done independently. In genomics studies, large-scale annotation was done for identification of genes and its corresponding protein sequences, after sequencing of the genome. The proteomics aims to elucidate the protein expression observed in different tissues under specific conditions along with an insight into various posttranslational modifications. In proteogenomics there is amalgamation of both genomics as well as proteomics for elucidating the gene structures.
Nutriproteomics
The study of proteins of nutritional values of an organism can be referred as nutriproteomics. It can be defined as the interaction of nutrients with the proteins by studying the effect of nutrients on protein synthesis, interaction of nutrients with proteins, and modulation of protein–protein interaction through nutrients.
Metabolism
The diverse chemical reactions leading to growth and development of an organism is often
referred to as metabolism and includes both anabolic and catabolic reactions.
Metabolomics
It is a branch of omics associated with study of metabolites of an organism in totality. This advancing field of science has much importance in pharmacological studies, functional genomics, toxicology, drug discovery, nutrition, cancer, and diabetes. As we know metabolites are the end result of all regulatory complex processes present in the cells hence metabolic changes represent reporters of alterations in the body in response to a drug or a disease.
Metabonomics
Metabonomics reflects the quantitative estimation of the metabolite of a particular organism and also includes the study of factors both exogenous and endogenous influencing the change in metabolite concentration. The exogenous factors such as environmental factors, xenobiotics, and endogenous factors such as physiology and development are predominantly considered in metabonomics. Like genomics, transcriptomics, and proteomics, metabonomics has immense potential in the discovery and development of new medicines.
Lipidomics
Lipidomics is the study of network of lipids and their interacting protein partners in organs, cells, and organelles. The lipidomic analysis is mainly done by mass spectrometry, commonly preceded by separation by liquid chromatography or gas chromatography.
Cytomics
Cytomics is the study of cytomes or the molecular single-cell phenotypes study resulting from genotype.
Pharmacogenomics
Pharmaconomics is the study of a complex genetic basis of interpatient variability in response to drug therapy. This subbranch of omics is an interesting field for pharmaceutical industries, clinicians, academicians, and patients as well. Using pharmacogenomics, the biopharmaceutical industries can improve the drug developmental process more rapidly and safely.
