What Is the Transcriptome and How it is Evaluated?

The concept of the transcriptome revolves around the complete set of transcripts present in a given cell type, tissue or organ and encompasses both coding and non-coding RNA molecules, although we often assume that it consists only of messenger RNAs (mRNAs) because of their importance in encoding proteins. Unlike the nuclear genome, whose composition and size are essentially static, the transcriptome often changes. The transcriptome is influenced by the phase of the cell cycle, the organ, exposure to drugs or physical agents, aging, diseases and a multitude of other variables, all of which must be considered at the time of its determination. However, it is precisely this property that makes the transcriptome useful for the discovery of gene function and as a molecular signature. In this chapter, we review the beginnings of transcriptome research, the main types of RNA molecules found in a mammalian cell, the methods of analysis, and the bioinformatics pipelines used to organize and interpret the large quantities of data generated by the two current gold-standard methods of analysis: microarrays and high-throughput RNA sequencing (RNA-Seq). Attention is also given to non-coding RNAs, using microRNAs (miRNAs) as an example because they physically interact with mRNAs and play a role in the fine control of gene expression.