Genomics, Transcriptomics, and Proteomics – The Basics
Genomics, transcriptomics, and proteomics are three branches of molecular biology that have become increasingly important in recent years. In this blog post, we would like to provide a brief overview that we hope will provide a useful introduction to each.
Perhaps the most commonly known of these three is genomics. Genomics is the large-scale study of all of the DNA that makes up a given organism or system. This can mean for example all of the DNA that makes up an entire single-cell organism, all of the DNA that makes up a particular cancer tumor, or all of the DNA that makes up an entire human being.
DNA is a double-stranded molecule made up of 4 types of nucleotides, often called the building blocks of DNA – adenine (A), thymine (T), cytosine (C), and guanine (G). While genomics typically refers primarily to the study of the sequence of these nucleotides, it can also touch areas such as epigenomics, heritable changes that relate instead to which parts of sequences are turned “on” or “off,” as opposed to deciphering only what the actual sequence is.
The introduction of next generation sequencing (NGS) for DNA sequencing has significantly accelerated the study of genomics, allowing for many discoveries that are advancing science and human health. This is particularly true with the advent of precision medicine. Precision medicine focuses on tailoring medical treatments, practices, products, and decisions to the individual, rather than using a one-size-fits-all model. Genomic data has been instrumental in this shift.
There are of course ethical considerations when it comes to genomics and genomic data as well. If an individual has their genome sequenced – where is this information stored? Who owns the information? And how can it be used to help (or unfortunately potentially to hurt) the individual? These are all questions that organizations, governments, and individuals are actively contemplating.
RNA is a single-stranded molecule that is transcribed from DNA, which leads us to discussing transcriptomics. Transcriptomics is the study of the complete set of RNA produced by the genome of a given organism or population of cells.
The transcriptome is generally studied under a certain set of circumstances (for example: what exactly happens to gene expression when liver cells are exposed to a certain drug?) or in a single cell, as is the case with single cell RNA sequencing.
NGS has changed the game here too. RNA studies were previously mainly conducted by microarray and microarray analysis, which is how higher throughput transcriptomics first became possible. Microarray analysis includes detection of nucleic acids by hybridization to probes on microchips.1 Microarray can only detect known sequences, however, whereas RNA sequencing with NGS can be used for discovery research.1 Levels of expression are generally better detected with RNA sequencing than microarray as well, since “background hybridization and probe saturation interfere with low-level and high-level detection”1 in microarray analysis.
There are three main types of RNA that are of interest when studying the transcriptome: messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA). Transcriptomics tells us which genes are being expressed, as well as the level or amount of expression of those genes.
The level of gene expression often determines how much of a particular protein is produced, bringing us to proteomics. Proteomics is the large-scale study of a set of proteins that are produced and/or modified in a given organism or system. Proteins are created by translating coding found in RNA. There are many proteomics methods used to study proteins, including protein sequencing, MALDI-TOF, and mass spectrometry. Perhaps the most important step in any of these proteomics methods is sample preparation. Protein fixation, protein stabilization, and protein purification are key to all downstream proteomic analysis. The particular protocol for protein purification will always depend on proteomic analysis method, but generally speaking it is a series of steps to isolate one or a few proteins from a more complex mixture of proteins and other molecules. Protein fixation and protein stabilization are generally achieved in a uniform way for the entire sample when a sample is initially processed after collection.
Whether you are using genomics, transcriptomics, proteomics, or a combination of these such as proteogenomics in your research, CellCover can help with sample preservation and stabilization.
For example in proteomics studies, fixing cells with CellCover for protein fixation and protein stabilization sets the stage for successful protein purification and downstream proteomic analysis.
CellCover was developed for fast “one step” stabilizing of biomolecules and is a non-toxic formulation for protecting the status of expression in human and animal cells and solid tissues, including tumors and cultured cells (adherent, suspension, or spheroids). DNA, RNA and proteins are all protected.
Most proteomics methods can benefit from protein fixation and protein stabilization with CellCover. Furthermore, if proteomic analysis reveals that further testing is necessary on DNA or RNA, the original sample fixed with CellCover can easily be revisited and subsequently purified for genomics or transcriptomics analysis.
1Tachibana, Chris. “Transcriptomics today: Microarrays, RNA-seq, and more.” Technology Feature. Science AAAS, 31 Jul. 2015. Web. https://www.sciencemag.org/features/2015/07/transcriptomics-today-microarrays-rna-seq-and-more