The Institute for the Physical and Chemical Research (RIKEN) Japan

Leader: Piero Carninci

Brief description of the organization:
RIKEN is a non-for profit independent organization, that receives the most of the research fund (>90%) from the Japanese government or Japanese funding Agencies. It is one of the largest and most prestigious Japanese research organizations. RIKEN include various institutes each one with his own focus, including genomics and neurobiology ( RIKEN is the leading Carninci's team is located at the RIKEN-Discovery Research Institute (DRI) and Carninci is double appointed at the RIKEN Genomic Science Center (GSC).

Main tasks attributed to the project:
Preparation of small-scale CAGE libraries for expression profiling, high-throughput sequencing, and bioinformatics analysis of the data and biological interpretation in particular regarding the promoter features, networks and noncoding RNA identified.

Previous experience relevant to the tasks:
The laboratory is very technology intensive, with a particular mission to develop key technologies for the transcriptional network. It has developed the first generation of the CAGE (cap-analysis gene expression) technology and is developing the next wave of CAGE technologies, by developing the protocols to use CAGE with high-throughput sequencers (454 Life Sciences and Solexa). This has permitted to implement expression profiling by providing much more function (identification of promoter activity and regulatory elements coupled to expression profiling). More recently, he has also developed micro-CAGE (unpublished), which allows preparing CAGE libraries from few hundred purified neurons (manuscript in preparation), isolated with laser-capture technologies. At the RIKEN-GSC laboratory, two main key activities are taking place. The first is very large-scale sequencing, which is essential for CAGE libraries. In fact the group has both the 454 and the Solexa sequencing instruments, and soon will also receive the new ABI Solid sequencer. This is a unique place in terms of concentration of sequencing technologies and expertise on how to use various technologies for expression profiling and other functional libraries. The team of Carninci at the GSC has been using the 454 Life Sciences sequencer for large scale CAGE profiling (and miRNA profiling) for more than 1.5 years: this expertise guarantees the start of the project without delays. Additionally, there is a very strong targeted bioinformatic support, with a collaborating group with 23 among scientists and technicians. They have developed the pipeline to assign CAGE tag to genes and genomes and to connect their expression with the microarrays expression profiling.

Selected recent publications:

  • Sandelin A, Carninci P, Lenhard B, Ponjavic J. Hayashizaki Y, Hume DA. Mammalian RNA Polymerase II Core Promoters' Insights From Genome-Wide Studies. Nature Rev. Genetics, 8:424-36. 2007

  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. The ENCODE Project Consortium. Nature, 447:799-816. 2007

  • Carninci P. Tagging mammalian transcription complexity. Trends Genet. 22:501-10. 2006.

  • Carninci P, et Al. Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data. Nat. Genetics, 38:626-35. 2006