• Winners
  • The 7th (2007) Yamazaki-Teiichi Prize Winner Biological Science & Technology

The 7th (2007) Yamazaki-Teiichi Prize Winner Biological Science & Technology

Development of the Cap-trapper, a Fundamental Technology to Isolate Full-length cDNAs and Annotate the Genome Function

winner Winner
Piero Carninci
Mar. 1989 Doctorate in Biological Science, University of Trieste
May 1990 Obtained national qualification on biology from University of Ferrara
Oct. 1990 Researcher at TALENT s.r.l
Oct. 1995 STA Fellow at RIKEN Tsukuba Life Science Center
Apr. 1997 Researcher at RIKEN
Apr. 2003 Concurrently acted as Senior Researcher at RIKEN's Discovery Research Institute and Genomic Sciences Center
Apr. 2006 Concurrently acting as Visiting Professor, Gunma University

Reason for award

To the present, the base sequence information for the genomes of a variety of animals, beginning with humans, plants and microorganisms has been clarified. Now, genome research has reached the step of elucidating the parts of the genome that are copied (transcribed) to RNAs and how transcription timing and quantity are controlled. In vivo RNA analysis will be indispensable to this step. However, being chemically unstable, RNAs are easily decomposed. Moreover, it is estimated that there are tens of thousands of regions on the genome that are copied to RNA. Because the expression (transcription) of them varies substantially in terms of time and space within biological activities, various hurdles accompany analysis of the entire picture of RNAs in vivo.
 First, to accurately determine the regions on the genome copied to RNAs, Dr. Carninci developed a method to synthesize full-length cDNAs which accurately copied mRNAs to chemically stable DNA. The making of full-length cDNA became possible by means of an innovative selection process known as "Cap-trapper." As an innovative technology for RNA analysis, the Cap-trapper method has been applied to numerous genome analysis projects useful to both academia and industry, leading to many useful and important genetic discoveries. This Cap-trapper technology has been commercialized and widely applied to the use of comprehensive human cDNA collections. It has been used significantly not only in academic research but for target identification in drug discovery and the like. The CAGE method that Dr. Carninci developed next by applying the Cap-trapper method is for selectively collecting and analyzing only the terminal moieties of full-length cDNA synthesized with the Cap-trapper method. With this method, the places and extent to which RNA is copied to the genome in response to a variety of vital activities can now be accurately and quantitatively measured. As a result, in addition to the major contribution made to medical research to elucidate molecular mechanisms in cancer, immune response and the like, it has demonstrated major impact on basic medicine and biology such as revealing that an extremely large amount of RNAs that do not code proteins (non-coding RNA) exists.
Riken and K.K. DNAFORM are jointly applying for and acquiring patents for full-length cDNA technology and the CAGE method. With RIKEN's full-length synthesis technology, a comprehensive human cDNA collection has been established. Commercialization of the CAGE method is progressing in terms of its application to the analysis of the expression of gene information, the diagnosis of new gene targets, and innovative detection methods. As stated previously, these technologies are being applied to Japan's Rice Genome Project and have had major impact on agricultural technology in terms of effective gene searching, molecular breeding and the like.
 The Cap-trap technology that Dr. Carninci developed is a good example of expanding from foundational technical development to academic research and finally to commercial application. In keeping with the clear contribution made to both industry and academia, Dr. Carninci has been awarded Yamazaki-Teiichi Prize in Biological Science and Technology.

Background of research and development

To properly understand genome sequence functions, it is extremely important to isolate RNAs and classify them as either transcribed and encoding a protein(mRNAs)or as structural or functional RNAs (non-coding RNAs). Unfortunately, computer analysis of genome sequences cannot accurately perform mapping of expressed RNAs. This is particularly striking for RNAs that have not been encoded as protein, as the sequences lack clear patterns. RNA sequence identification is one of the most pressing problems in genome analysis. Its realization would enable RNA structure and expressed proteins to be elucidated; the areas that regulate transcription activity, known as promoters, to be identified; and mapping of genes to be done.
Although it is possible to partially identify these RNAs using cloning methods for complementary DNAs (cDNAs), until the mid 1990s, there was no convenient technology for isolating full-length cDNA from a complete copy of mRNA. Until this time, only 10%~20% of the individual cDNA clones in cDNA libraries were full-length cDNA. It was impossible to draw biological and functional conclusions and infer the true structure of genes. However, full-length cDNA contains all of the information of the original mRNA, from the transcription start point to the end point. By superimposing these sequences on genomes via computer, detailed gene structure can be determined. If full-length cDNA can be used, it will be the source for a variety of biological research, in addition to research on protein expression, structural determination and other downstream functions.


To tackle the problem of cloning full-length cDNAs, the prizewinner developed the "Cap-Trapper" technology to add biotin to cap structure at the 5' ends of mRNAs. This method uses biotin to efficiently isolate full-length cDNAs, which it separates from non-full-length cDNAs. Based on this technology, Carninci et al developed even more advanced technology to separate the full-length cDNAs from extremely rare expressions of RNAs. By doing so, they discovered that at least half of mammalian RNAs do not encode proteins, but have structural and regulatory functions akin to the RNAs that are the antisense of the expressed mRNAs. This led to the even more important discovery that RNAs have regulatory functions.
The prizewinner used Cap-Trapper technology to develop Cap Analysis Gene Expression (CAGE) technology. The short stretches separated from the 5' ends of full-length cDNAs are fundamental to this technology. These tags are ideal for large-scale base-sequence determination, and genome sequences can be mapped via computer. With this operation, the RNA transcription start point that is near the area that controls RNA transcription can be identified. As this neighboring area, which is called the core promoter area, controls RNA expression, CAGE technology, which also measures RNA expression, has made possible research on RNA expression together with the regulatory region, called promoter.

Meaning of the achievements

With the Cap-Trapper technology, Carninci et al made the RIKEN's full-length cDNA collections. These collections include full-length cDNA clones for mice, humans, rats, chickens, fruit flies, honey bees, rice, arabidopsis thaliana, and other various model organisms. cDNAs are important resources not only for genome annotation but for cDNA microarrays, protein expression, protein interactions, in-vitro and in-vivo full-length cDNA expression systems and other functional research. The full-length cDNA collection for mice changed the way of thinking concerning human genome production. In fact, nearly all of the mammal genomes are transcribed to various types of duplicated RNA transcripts, of which over half of the transcribed RNAs of mammal genome does not encode protein. At least 70% of mammal genes have a sense-antisense transcription. Antisense RNA affects the expression level of sense RNA. There are over 181,000 different transcripts, and at least 240,000 regulatory regions (promoters) have been mapped and analyzed using CAGE technology. Clustering expressed with promoters is effective and important for transcription network analysis and is indispensable to methodical and comprehensive approaches to biology. CAGE technology is used in both domestic and international projects. This original technology is also one of the technologies that is essential to the Genome Network Project and to ENCODE, an NIH-led competitive international project under.
These technologies have been patented and are used commercially by K.K. DNAFORM, a venture program of RIKEN, which commercialized the full-length cDNA and CAGE technologies.