Transcriptomic analysis of genes: expression and regulation

The transcriptomic profile of a given organism is the set of RNA molecules expressed under certain conditions. It varies based on the biological process, stage of development, and environment. Different tools have been developed to measure gene transcription and expression in specific cellular states. Sequencing technologies vary from low to high throughput and allow whole-transcriptome analysis. RNA-seq coupled with bioinformatics approaches has been widely used in different studies to reveal the exact process of cellular transcription. RNA-seq data have also recently been used for modeling gene interactions through coexpression networks, a powerful method for making functional inferences about genes involved in a certain process. In this chapter, the evolution of RNA- seq studies, the methods used to isolate and sequence RNA, the programs necessary to assemble the data, and the essential steps for differential expression analysis are described, and the advantages and limitations of these methods are discussed. Herein, we report the applications of transcriptome studies for biotechnological purposes. For example, we describe the potential applications and methods of production of biomolecules from fungi and bacteria by genetic engineering and the development of treatments for human diseases, showing the importance of transcriptomic analyses in revealing the roles of gene expression control.