Functional Genomics Technology Team
Team Leader
Piero CARNINCI (Ph.D.)
Breakthroughs in science depend on the development of novel technologies to solve outstanding biological problems. The director of the team has 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.
These developments will be done in collaboration with other teams and units and external collaborator, with particular hope to contribute to the development of the Omics Science Center as an internationally recognized institute and serve the community by ultimately implementing biomedical sciences and increasing our knowledge.
- Characterization of Isolated Neurons transcriptome with nano-scale cap-analysis gene expression (nano-CAGE)
- Identification and general properties of mammalian promoters
- Function of non-coding RNA, including retrotransposon-derived RNAs
- Application of the CAGE technology to human health
- June 14, 2010
- RIKEN and SISSA develop new biological analysis methods
- Faulkner, G.J., Kimura, Y., Daub, C.O., Wani, S., Plessy, C., Irvine, K.M., Schroder, K., Cloonan, N., Steptoe, A.L., Lassmann, T., Waki, K., Hornig, N., Arakawa, T., Takahashi, H., Kawai, J., Forrest, A.R., Suzuki, H., Hayashizaki, Y., Hume, D.A., Orlando, V., Grimmond, S.M., Carninci, P.:
" The regulated retrotransposon transcriptome of mammalian cells."
Nat. Genet. 41:563-71-.2009. - Taft, R., Glazov, E.A., Cloonan, N., Simons, S., Stephen, S., Faulkner, G., Lassmann, T., Forrest, A.F.F., Grimmond, S.M., Schroder, K., Irvine, K., Arakawa, T., Nakamura, M., Kubosaki, A. Hayashida, K., Kawazu, C., Murata, M., Nishiyori, H., Fukuda, S., Kawai, J., Daub, C.O., Hume, D.A., Suzuki, H., Orlando, V., Carninci, P., Hayashizaki, Y. and Mattick, J.:
" Tiny RNAs associated with transcription start sites in animals."
Nat. Genet.41:572-8.2009. - Suzuki, H., Forrest, A.R., van Nimwegen, E., Daub, C.O., Balwierz, P.J., Irvine, K.M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M.J., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V.B., Bauer, D., Beckhouse, A.G., Bertin, N., Björkegren, J., Brombacher, F., Bulger, E., Chalk, A.M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P.G., Essack, M., Faulkner, G.J., Fink, J.L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S.M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hörnquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M.C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., Macpherson, C., Maeda, N., Maher, C.A., Maqungo, M., Mar, J., Matigian, N.A., Matsuda, H., Mattick, J.S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schönbach, C., Schwartz, A.S., Semple, C.A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M.J., Taft, R.J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M.S., Teasdale, R.D., Tegnér, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C.A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D.A., Riken Omics Science Center, Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J., Hayashizaki, Y.:
" The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line."
Nat Genet. 41:553-62. 2009. - Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T.T., Eric, Tang. M.H., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M., Hayashizaki, Y., Gustincich, S., Sandelin, A., Carninci, P.:
" Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. "
Genome Res. 19:255-65.2009. - The ENCODE Project Consortium.
" Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project."
Nature, 447:799-816. 2007 - Sandelin, A., Carninci, P., Lenhard, B., Ponjavic, J., Hayashizaki, Y., and Hume, D.A.:
" Mammalian RNA Polymerase II core promoters - insights from genome-wide studies."
Nature Rev. Genetics 8:424-36. (2007). - Carninci, P.
" Tagging mammalian transcription complexity. "
22:501-10. 2006.Trends Genet. Review(2006). - Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, S., Ponjavic, J., Semple, C., Taylor, M., Engstrom, P., Frith, M.C., Forrest, A.R.R., Alkema, W., Tan, S.L., Plessy, C., Kodzius, R., Ravasi, T., Kasukawa, T., Fukuda, S., Kanamori-Katayama, M., Kitazume, Y., Kawaji, H., Kai, C., Nakamura, M., Konno, H., Nakano, K., Mottagui-Tabar, S., Arner, P., Chesi, A., Gustincich, S., Persichetti, F., Suzuki, H., Grimmond, S.M., Wells, C.A., Orlando, V., Wahlestedt, C., Liu, E.T., Harbers, M., Kawai, J., Bajic, V.B., Hume, D.A., and Hayashizaki, Y.:
" Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data."
Nat. Genetics, 38:626-35. (2006). - Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., Hayashizaki, Y., and Carninci, P.:
" CAGE: cap analysis of gene expression."
Nat Methods. 3:211-22. (2006). - Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V.B., Brenner, S.E., Batalov, S., Forrest, A.R.R., Zavolan, M., Davis, M J., Wilming, L.G., Aidinis, V., Allen, J.E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R.N., Bailey, TL., Bansal, M., Baxter, L., Beisel, KW., Bersano, T., Bono, H., Chalk, A.M., Chiu, K.P., Choudhary, V., Christoffels, A., Clutterbuck, D.R., Crowe, ML., Dalla, E., Dalrymple, B.P., de Bono, B., Della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C.F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T.R., Gojobori, T., Green, R.E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, TK., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S.P.T., Kruger, A.F., Kummerfeld, S.K., Kurochkin, I.V., Lareau, L.F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan, Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K.C., Pavan, W.J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J.F., Ring, B.Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S.L., Sandelin, A., Schneider, C., Schönbach, C., Sekiguchi, K., Semple, C.A.M., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, SL., Tang, S., Taylor, MS., Tegner, J., Teichmann, S.A., Ueda, H.R., van Nimwegene, E., Verardo, R., Wei, C.L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S.M., Teasdale, R.D., Liu, ET., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J.S., Hume, D.A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., and Hayashizaki, Y.:
" The Transcriptional Landscape of the Mammalian Genome."
Science, 309:1559-63. (2005).