Tag-based approaches for transcriptome research and genome annotation

With the increasing number of whole genome sequences available, genomic research has shifted toward the annotation of functional elements and transcribed regions. Thus, the related field of transcriptome research requires accurate methods for the profiling of genes that are not biased by known sequence information, and that also allow for the identification of promoter regions. Starting with serial analysis of gene expression (SAGE), methods making use of short sequencing tags have greatly contributed to transcriptome studies. Here we review recent developments in the use of short sequencing tags in expression profiling, gene discovery and genome annotation. These tags are obtained from the 5' end of mRNAs, both terminal ends of mRNAs, or genomic regions. The 5' end-specific tags, with their ability to identify transcripts along with their transcriptional start sites, will be of particular interest for gene network studies and may become one of the most important approaches in systems biology.