RIKEN Center for Life Science Technologies

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Labs & Technologies

Transcriptome Technology Team

* Due to the reorganization starting as new centers in April 2018, this laboratory is now belong to the Center for Integrative Medical Sciences. As for the latest information, please see the following URL below.
> The webpage of Laboratory for Transcriptome Technology, Center for Integrative Medical Sciences

Team Leader
Piero Carninci  Ph.D.

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045

2_1_carninci.png

Research Area

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.

Main Publications List

2

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.
Science, 347(6225), 1010-1014 (2015).
3

Deep transcriptome profiling of mammalian stem cells supports a key regulatory role for retrotransposon in pluripotency maintenance

Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, Suzuki H, Wei CL, Koseki H; FANTOM Consortium, Hasegawa Y, Forrest AR, Carninci P.
Nature Genetics, 46(6), 558-566 (2014).
4

A promoter-level mammalian expression atlas

FANTOM Consortium and the RIKEN PMI and CLST (DGT)
Nature, 507(7493), 462-470 (2014).
5

An atlas of active enhancers across human cell types and tissues

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.
Nature, 507(7493), 455-461 (2014).
6

Two independent transcription initiation codes overlap on vertebrate core promoters.

Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B.
Nature, 507(7492), 381-385 (2014).
7

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S.
Nature, 491(7424), 454-457 (2012).
8

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M.
Nature, 489(7414), 57-74 (2012).
9

Site-specific DICER and DROSHA RNA products control the DNA-damage response.

Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P, d'Adda di Fagagna F.
Nature, 488(7410), 231-235 (2012).
10

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

Takahashi H, Lassmann T, Murata M, Carninci P.
Nat Protoc, 7(3), 542-561 (2012).

>>>All Publications

Member  *concurrent

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CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Transcriptome Technology Team, please visit the following websites.


> The webpage of Laboratory for Transcriptome Technology, Center for Integrative Medical Sciences [http://www.ims.riken.jp/labo/60/index.html]