Transcriptome Technology Team

We will develop technologies to comprehensively detect non-coding RNAs and comprehensively screen their functions. Using those technologies, we will explore regulatory interactions of ncRNAs within cells, with particular emphasis on the interaction of non-coding RNA with chromatin, retrotransposition and ncRNAs having a role in the regulation of protein synthesis. These technologies will be important for the development of cell conversion methods. Additional emphasis will be on standardization of transcriptome technologies like CAGE, to make a universal and finely quantitative transcriptome technology. Such standardization is essential for the identification of novel biomarkers and drug target candidates.

Research Fields

Biology & Biochemistry / Molecular Biology & Genetics / Immunology / Plant & Animal Science / Neuroscience & Behavior / Computer Science

Research Subjects

• Standardization and Automation of Cap-Analysis Gene Expression (CAGE)
• Development of methods to globally detect and manipulate regulatory RNAs on Chromatin
• Identification of expressed retrotransposons and their role in genome variability and regulation

Publications

1. H Takahashi, T Lassmann, M Murata, P Carninci
   5' end-centered expression profiling using Cap-analysis gene expression and next-generation sequencing
   Nature Protocols, 7(3), 542-561 (2012)
2. B Lenhard, A Sandelin, P Carninci
   Metazoan promoters: emerging characteristics and insights into transcriptional regulation
   Nature Reviews Genetics, 13, 233-245 (2012)
3. C Carrieri, L Cimatti, M Biagioli, A Beugnet, S Zucchelli, S Fedele, E Pesce, I Ferrer, L Collavin, C Santoro, AR Forrest, P Carninci, S Biffo, E Stupka, S Gustincich
   Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
   Nature, 491, 454-457 (2012)
4. S Djebali, C Davis, J Lagarde, A Dobin, A Merkel, C Zaleski, T Lassmann, W Lin, F Schlesinger, C Xue, A Tanzer, A Mortizavi, J Khatun, F Kokocinsk, RF Abdelhamid, T Alioto, M Baer, P Batut, K Bell, I Bell, S Chakrabortty, X Chen, J Chrast, J Curado, T Derrien, J Drenkow, E Dumais, J Dumais, R Duttagupta, M Fastuca, K Fejes-Toth, P Ferreira, S Foissac, M Fullwood, H Gao, D Gonzalez, A Gordon, H Gunawardena, C Howald, R Johnson, P Kapranov, C Kingswood, O Luo, G Marinov, E Park, J Preall, P Ribeca, B Risk, D Robyr, M Roeder, M Sammeth, L See, A Shahab, J Skancke, A Suzuki, H Takahashi, H Tilgner, D Trout, N Walters, H Wang, B Williams, J Wrobel, Y Yu, X Ruan, Y Hayashizaki, J Harrow, T Hubbard, A Reymond, S Antonarakis, G Hannon, M Giddings, Y Ruan, B Wold, P Carninci, R Guigo Serra, TR Gingeras
   Landscape of transcription in human cells
   Nature, 489, 101-108 (2012)
5. C Plessy, G Pascarella, N Bertin, A Akalin, C Carrieri, A Vassalli, D Lazarevic, J Severin, C Vlachouli, R Simone, GJ Faulkner, J Kawai, CO Daub, S Zucchelli, Y Hayashizaki, P Mombaerts, B Lenhard, S Gustincich, P Carninci
   Promoter Architecture of Mouse Olfactory Receptor Genes
   Genome Research, 22, 486-497 (2011)
6. C Plessy, N Bertin, H Takahashi, R Simone, M Salimullah, T Lassmann, M Vitezic, J Severin, S Olivarius, D Lazarevic, N Hornig, V Orlando, I Bell, H Gao, J Dumais, P Kapranov, H Wang, C Davis, TR Gingeras, J Kawai, CO Daub, Y Hayashizaki, S Gustincich, P Carninci
   Linking new promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
   Nature Methods, 7, 528-534 (2010)
7. GJ Faulkner, Y Kimura, CO Daub, S Wani, C Plessy, KM Irvine, K Schroder, N Cloonan, AL Steptoe, T Lassmann, K Waki, N Hornig, T Arakawa, H Takahashi, J Kawai, AR Forrest, H Suzuki, Y Hayashizaki, DA Hume, V Orlando, S Grimmond, P Carninci
   The regulated retrotransposon transcriptome of mammalian cells
   Nat Genet, 41(5) , 563-571 (2009)
8. P Carninci, A Sandelin, B Lenhard, S Katayama, K Shimokawa, J Ponjavic, C Semple, M Taylor, PG Engström, MC Frith, AR Forrest, WB Alkema, SL Tan, C Plessy, R Kodzius, T Ravasi, T Kasukawa, S Fukuda, M Kanamori-Katayama, Y Kitazume, H Kawaji, C Kai, M Nakamura, H Konno, K Nakano, S Mottagui-Tabar, P Arner, A Chesi, S Gustincich, F Persichetti, H Suzuki, S Grimmond, C Wells, V Orlando, C Wahlestedt, ET Liu, M Harbers, J Kawai, VB Bajic, DA Hume, Y Hayashizaki
   Genome-wide analysis of mammalian promoter architecture and evolution
   Nat Genet, 38(6), 626-635 (2006)
9. S Katayama, Y Tomaru, T Kasukawa, K Waki, M Nakanishi, M Nakamura, H Nishida, C C Yap, M Suzuki, J Kawai, H Suzuki, P Carninci, Y Hayashizaki, C Wells, M Frith, T Ravasi, K C Pang, J Mattick, D A Hume, L Lipovich, P G Engström, Y Mizuno, M A Faghihi, A Sandelin, A M Chalk, S Mottagui-Tabar, Z Liang, B Lenhard and C Wahlestedt
   Antisense transcription in the mammalian transcriptome
   Science, 309, 1564-1566 (2005)
10. P Carninci, T Kasukawa, S Katayama, J Gough, M C Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, V B Bajic, S E Brenner, S Batalov, A R R Forrest, M Zavolan, M J Davis, L G Wilming, V Aidinis, J E Allen, A Ambesi-Impiombato, R Apweiler, R N Aturaliya, T L Bailey, M Bansal, L Baxter1, K W Beisel, T Bersano-Begey, H Bono, A M Chalk, K P Chiu, V Choudhary, A Christoffels, D R Clutterbuck, M L Crowe, E Dalla, B P Dalrymple, B de Bono, G Della Gatta, D di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, C F Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, T R Gingeras, T Gojobori, R E Green, S Gustincich, M Harbers, Y Hayashi, T K Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, K Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, M Katoh, Y Kawasawa, J Kelso, H Kitamura, H Kitano, G Kollias, S P T Krishnan, AF Kruger,　S K Kummerfeld, I V Kurochkin, L F Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M Madan Babu, M Madera, L Marchionni H Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, S Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, V Orlando, K C Pang, W J Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, J F Reid, B Z Ring, M Ringwald, B Rost, Y Ruan, S L Salzberg A Sandelin, C Schneider, C Schönbach, K Sekiguchi, C A M Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, K Sugiura, R Sultana, Y Takenaka, K Taki, K Tammoja, S L Tan, S Tang, M S Taylor, J Tegner, S A Teichmann, H R Ueda, E van Nimwegene, R Verardo, C L Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, S M Grimmond, R D Teasdale, E T Liu, V Brusic, J Quackenbush, C Wahlestedt, J S Mattick, D A Hume, C Kai, D Sasaki, Y Tomaru, S Fukuda, M Kanamori-Katayama, M Suzuki , J Aoki1, T Arakawa, J Iida, K Imamura, M Itoh, T Kato, H Kawaji, N Kawagashira, T Kawashima, M Kojima, S Kondo, H Konno, K Nakano, N Ninomiya, T Nishio, M Okada, C Plessy, K Shibata, T Shiraki, S Suzuki, M Tagami, K Waki, A Watahiki , Y Okamura-Oho, H Suzuki, J Kawai, Y Hayashizaki
    The transcriptional landscape of the mammalian genome
    Science, 309, 1559-1563 (2005)