Lecture 7: The World of Omics - Transcriptomics and Metabolomics PDF

Lecture 7: The World of Omics Transcriptomics and Metabolomics Transcriptomics Transcriptomics is the study of the 'transcriptome,' a term now widely understood to mean the complete set of all the ribonucleic acid (RNA) molecules (called transcripts) expressed in some given entity, such as...

Lecture 7: The World of Omics Transcriptomics and Metabolomics Transcriptomics Transcriptomics is the study of the 'transcriptome,' a term now widely understood to mean the complete set of all the ribonucleic acid (RNA) molecules (called transcripts) expressed in some given entity, such as a cell, tissue, or organism. Transcriptomics Gene – regulation of metabolism - important to know their expression level in order to understand the physiology of the cell Gene expression - Northern blot annealing of fractionated mRNA with the cognate pieces of DNA, and reverse transcriptase–PCR, in which mRNA is used as a template to produce cDNA, which is then amplified by PCR. Still used when we already know the mechanism of regulation in precise detail and when we want to know the expression level of the genes involved. Transcriptomics However, when the regulation mechanism is not known entirely, examining the expression levels of only a few selected genes becomes pure guesswork has led to many wrong conclusions. Transcriptomics A microarray is a laboratory tool used to detect the expression of thousands of genes at the same time. DNA microarrays are microscope slides - with thousands of tiny spots containing a known DNA sequence or gene. Gene chips or DNA chips. Transcriptomics The affinity of the mRNA to a cognate piece of DNA fragment is obviously affected by the length, base composition, and other characteristics of the probe The binding itself cannot be used as the measured marker However, we are usually interested in changes in transcription patterns Comparison can be made by labeling the mRNA populations from two samples (query and reference) by different fluorescent dyes. Proteomics Expression of genes - by quantitating their transcription - transcriptomics approach. However, mRNA must be translated, and translational control adds an important step to the expression of genetic information. In higher eukaryotes, many proteins are processed mainly by proteolytic cleavage, and various posttranslational modification steps also intervene. These steps are thought to increase the complexity of the “proteome” Proteomics  Proteomics and mass spectrometry Proteomic analysis Mass spectrometry, which measures the Mass-ratio of ions in a vacuum Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) MALDI is the ionization method used, and time-of-flight (TOF) Protein-to-protein interactions Protein arrays Metabolomics and systems biology Expression levels of proteins - levels of many metabolites – Metabolomics Mass spectroscopy and nuclear magnetic resonance (NMR) From the perspective of biotechnology, metabolomics becomes significant only when it is combined with transcriptomics and proteomics. Integrate all the “omics” information together, in the direction of systems biology Metabolomics- supplies an exceptionally sensitive indicator of phenotypes