Transcriptome Analysis through Expressed Sequences

1. Transcriptome Analysis Recent advances in sequencing, computational biology, and information science have brought great new opportunities in biological research. One of the opportunities is that researchers are able to apply a systematic approach towards understanding some of the objects or phenomena in molecular biology/genetics and modern medicine. Not long ago, such a systematic approach was restricted to very few sub-disciplines in biological and medical sciences, such as anatomy or taxonomy, where scientists and researchers have been trying to catalogue and investigate every component of a given system. This new opportunity specifically refers to current research interest on various "-omes, " including genome, transcriptome, proteome, metabolome, and others. Genome research addresses the physical sequence, the alternation, and the evolution of genetic materials, which are composed of DNA in most species. Transcriptome research (Velculescu et al., 1995) focuses on the investigation of the expression of genetic materials and its regulation. A transcriptome is a collection of expressed sequences in a particular cell at a specific time point. A related concept is the " whole transcriptome, " which refers to the complete set of RNA molecules derived from the genome during the lifetime of an organism. The expressed sequences could be mRNA, tRNA, rRNA, or other RNA species. While current transcriptome analysis focuses on mRNA molecules, which code for proteins, transcriptome is much more than proteome (the collection of all proteins in an organism), especially since more and more non-protein coding RNA molecules, besides tRNA and rRNA, have been identified recently For instance, there has been a great interest in the significant role of small interference RNA in gene silencing (Plasterk, 2002). Furthermore, a large percentage of mouse genes are likely to be non-protein coding and the non-coding genes are likely to be conserved across different species and unspliced (The FANTOM Consortium, 2002). Genome and transcriptome are two related, yet different concepts. In a particular cell, the genome undergoes little change during transitions, such as cell division and cell differentiation. A transcriptome in a cell, on the other hand, is dynamic and is changed both spatially and temporally. While different tissues or cell types in an organism have the same genome (except for somatic mutations), their transcriptomes could be vastly different. This dynamic and transitive nature of a transcriptome requires unique technologies and computational consideration. Various experimental and computational techniques have been employed to investigate the