3rd generation transcriptomics - CAGE

Monday Noon Seminar: Dr. Piero Carninci, RIKEN Yokohama Institute
12:00 PM-1:00 PM (Lecture Theatre)

3rd generation transcriptomics - CAGE

Breakthroughs in science depend on the development of novel technologies to solve outstanding biological problems. We have previously developed key technologies including the cap-trapper to comprehensively clone full-length cDNAs and the cap-analysis gene expression (CAGE). The mission of the Functional Genomics Technology Team is to develop novel original approaches to comprehensively study genes, their products and their interactions. The approaches should address biological questions that cannot be addressed with technologies that are the state of the art today. In contrast with classic approaches considering one gene at the time, our mission is to develop approaches that aim at targeting biological problem as systems. This requires to comprehensively analyzing various biological aspects.
The members of the laboratory are engaged in the development of original approaches and to design, propose and realize original genomics technologies and apply these to challenging biological problems. These include the discovery, validation and analysis of novel classes of non-coding RNAs; establishing single-cell CAGE methods and its application to reduced biological samples; and data mining, with particular interest at identifying biological patterns and rules, including genome-wise analysis of novel classes of RNAs and their network. To address these genomics approaches for samples derived from living cells in their biological context, particular emphasis consists in the miniaturization of these technologies, to analyze systematically the biology of few or single isolated cells, such as the characterization of the molecular networks of individual neurons, included in a larger cellular networks. Going beyond simple expression profiling, the ultimate mission is to understand the complex relationships between gene expression regulation, the non-coding RNA world, the epigenome and the biological output.


http://genome.gsc.riken.jp/osc/english/members/Piero_Carninci.html

http://fantom.gsc.riken.jp

The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4.