We have developed cap-analysis gene expression (CAGE) to simultaneously map mRNAs and non-coding RNAs transcription starting sites (TSSs) and measure their expression at each different promoters. Since CAGE shows single nucleotide resolution, we can use this technology to comprehensively measure gene expression at each TSSs. Due to this unprecedented resolution, we have learned that promoters use different regulatory elements in different cells and tissues. Using CAGE, we can also infer the transcriptional networks that regulate gene expression in each different cell type. For its high resolution to map TSSs, CAGE has been used extensively in the ENCODE and modENCODE projects.

In the FANTOM5 project, we have applied CAGE on a comprehensive panel of human and mouse primary cells and other tissues, resulting in a very broad map the promoterome and regulatory networks. Our map reveals the existence of more than 180,000 promoters and 45,000 enhancers, which are often tissue specific. The FANTOM5 database is one of the broadest expression database available to the community.

Additionally, we have determined the pattern of expression of retrotransposon elements (RE), which are likely to have a regulatory role. As example, some families of LTR retrotransposon elements are specifically expressed in ES and iPS cells, where they have a role in maintenance of pluripotency. Future FANTOM projects will be focusing to broadly understand the function and the interaction with cell regulatory networks of these RNAs in several primary cells, with the purpose to create the broadest database of functional lncRNAs.