トランスクリプトーム研究チーム

細胞内の全DNAの塩基配列情報をさす「ゲノム」に対し、細胞内の全転写産物（全RNA）を「トランスクリプトーム」とよびます。トランスクリプトームの大半はタンパク質の情報を持たないノンコーディングRNA(ncRNA)であり、エピジェネティック制御やタンパク質合成制御、幹細胞性の制御など様々な機能に関わっています。当チームは、ncRNAを網羅的に検出する技術やその機能を網羅的に調べる技術を開発し、新たなバイオマーカーの同定や薬剤候補因子の発見、細胞制御、細胞変換に応用します。ncRNAクロマチン、レトロトランスポゾンのncRNAによる制御や、ncRNAのタンパク質合成における制御を調べます。また定量的な発現解析手法であるCAGE技術等のトランスクリプトーム技術の標準化を進めます。

研究分野

生物学 & 生化学 / 分子生物 & 遺伝学 / 免疫学 / 植物 & 動物学 / 神経科学 & 行動科学 / コンピューター科学

研究テーマ

• Cap-Analysis Gene Expression (CAGE)法の標準化および自動化
• クロマチンに結合する調節RNAを広範に検出し、操作する手法の開発
• 発現しているレトロトランスポゾンを同定し、ゲノム多様性とゲノム制御における役割を 解明する

主要論文

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)