RNA Sequencing

 

Also known as whole transcriptome shotgun sequencing (WTSS), RNA sequencing (RNA seq) is a recently developed approach used to investigate the expression profile and abundance of RNA species from cells harvested at particular stages/time points. Through RNA seq, the extent and complexity of eukaryotic and prokaryotic transcriptomes have been explored and become appreciated in the past few years. With the technological advance in NGS platforms, it represents a more precise and rapid, unbiased and less sample-demanding means to discover novel transcripts and measure the abundance of transcripts than any previously developed methods such as microarrays.

 

With the trend in complete bacterial genomes, the biological question will undoubtedly shift along the central dogma from the level of genes to transcripts, which advance the delineation of operons and untranslated regions and other novel genetic elements, facilitating and improving sequence annotation and allow investigation of how genetic variation influences regulation and function of related bacteria, especially bacterial strains with huge genetic variation and/or biochemical properties. By aligning the reads across splice junctions, RNA seq can identify isoforms, novel transcripts and gene fusions. Additional sample preparation strategies can be applied for furthering investigation on details such as strand information. As gene expression in a cell is highly dynamic, comparative transcriptome studies would allow the identification of genes/pathway of interest based on investigation and analyses on differential expression (DE) and co-expression networks.