Transcriptomics Overview

Study Notes

Transcriptomics studies the transcriptome, the complete set of RNA molecules expressed in a cell, tissue, or organism.
It's crucial to understand gene expression levels to comprehend a cell's physiology.
Gene expression is often studied using Northern blotting.
Northern blotting involves annealing fractionated mRNA to DNA fragments, reverse transcriptase-PCR, and PCR amplification.
This method is used when the regulation mechanism is well understood and precise gene expression levels are required.
If regulation isn't fully understood, examining the expression of a few genes might lead to inaccurate conclusions.
Modern methods like microarrays (DNA microarrays) are used to simultaneously examine thousands of genes.
Microarrays are microscope slides with many tiny spots, each with a known DNA sequence or gene.
DNA microarrays can quickly determine the expression level of thousands of genes.
Another method for measuring transcription patterns involves gene chips or DNA chips.
mRNA binding to DNA fragments is affected by length, base composition, and probe characteristics.
mRNA populations can be compared by labeling them with fluorescent dyes. This reveals changes in transcription patterns.

Studying gene expression involves analyzing their transcription levels.
However, RNA needs translation, and translational control, which adds an additional crucial step to gene expression analysis.
Many eukaryotic proteins undergo proteolytic cleavage and post-translational modifications, increasing the complexity of proteins in the proteome.
Proteomes are the complete set of proteins expressed within a cell, tissue, or organism.
Modern proteomic analysis uses mass spectrometry, measuring the mass-to-charge ratio of ions in a vacuum.
Technologies like matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) are common in proteome analysis.
MALDI is a commonly used ionization method, combined with time-of-flight (TOF).
Protein arrays are also employed in proteomic research.
Proteomics often involves studying protein-protein interactions.

Metabolomics looks into the levels of metabolites, which are directly linked to protein expression levels.
Integrating metabolomics with transcriptomics and proteomics gives crucial insights into systems biology.
Mass spectrometry and nuclear magnetic resonance (NMR) are used in metabolomics.
Metabolomics becomes significant in biotechnology when combined with other "omics" approaches.
Metabolomics provides a sensitive way to observe phenotypes or characteristics of an organism, making it a valuable tool in systems biology.