Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome

The findings of the FANTOM3/Genome Network project have redefined the landscape of the mammalian transcriptome by introducing an extensive collection of novel cDNAs and millions of sequenced tags corresponding to 5′- and 3′-ends of mRNAs. This issue of PLoS Genetics includes a special collection of articles that explore the transcriptome complexity being revealed by work on the FANTOM3 dataset. Besides revealing staggering complexity, analysis of this collection is providing an increasing number of novel mRNA classes, expressed pseudogenes, and bona fide noncoding variants of protein-coding genes. In addition, new types of regulatory logic have emerged, including sense–antisense mechanisms of RNA regulation. This high-resolution cDNA collection and its analysis represent an important world resource for discovery, and demonstrate the value of large-scale transcriptome approaches towards understanding genome function.