シャルル(Charles) プレシ(Plessy) — Population transcriptomist

ゼブラフィッシュを用いて初めて発生遺伝学の研究を行って以来、全トランスクリプトーム解析およびその技術に強い関心を持つようになった私は、さらなる研究を行うため2004年に理化学研究所に移り、プロモーターのプロファイリングおよび遺伝子ネットワーク推定のためのハイスループット・メソッド、特にCAGE法(Cap Analysis Gene Expression)の研究を行ってきました。

I have developed a miniaturized version of CAGE, termed nanoCAGE, to analyse small samples yielding only nanograms of RNA (Plessy et al., 2010). In the same manuscript, we also introduced its paired-end variant, CAGEscan, which we use to associate novel promoters with annotations. Since then, we have kept improving or expanding these techniques, by updating the protocol (Salimullah et al., 2011), reducing the sequence bias introduced by the molecular barcodes (Tang et al., 2013), combining multiple cap-enrichment steps (Batut et al., 2013), and benchmarking the use of locked nucleic acids for template switching (Harbers et al., 2013).

I have complemented my work on CAGE with the development of a gene-centred technique for detecting promoters, termed Deep-RACE (Olivarius et al., 2009, Plessy et al., 2012), which we used to validate our discovery of the pervasive expression of retrotransposons detected by CAGE (Faulkner et al., 2009). With contributions related to CAGE development and analysis, I am member of the FANTOM consortium since FANTOM3.

Together with my colleagues at RIKEN and collaborators in the field of neuroscience, I have applied nanoCAGE to the study of single neuron cell types, for instance the olfactory neurons (Plessy et al., 2012), or in dopaminergic cells, where we could demonstrate the expression of haemoglobin in the midbrain (Biagioli et al., 2009). We are also exploring the sub-cellular localisation of RNA in Purkinje neurons (Kratz et al, 2014). In parallel with this promoter-centric work, I am also exploring the huge repertoire of the T cell antigen receptors.

また、私はオープンソース・フリーソフトウェアの熱心な支持者でもあり、Debian Medプロジェクトではバイオインフォマティクス・ツールのパッケージングにも貢献。これらのツールはDebian (Möller et al., 2010) およびDebianから派生したUbuntuや(cloud)Bio-Linuxで再配布されています。尚、理研の研究員としての貢献、その他の活動に関する電子署名には、GPGキー番号B3443334を使用しています。

私は極力多くの細胞をサンプリングすることに焦点を絞ったPopulation Transcriptomics (Plessy et al., 2013) の手法を用いて単一細胞に関する当研究を発展させるべく、理化学研究所ライフサイエンス技術基盤研究センター機能性ゲノム解析部門ゲノミクス微量技術開発ユニットのリーダーとして、2013年4月、新たな開発サイクルを開始しました。

My ORCID ID is 0000-0001-7410-6295.

最新ニュース

C1 CAGE released.
Posted
Lecture on single cells
Posted
Lecture on non-translated RNAs
Posted
ECRO 2013で発表
Posted

最近の論文

Taguchi A, Nagasaka K, Kawana K, Hashimoto K, Kusumoto-Matsuo R, Plessy C, Thomas M, Nakamura H, Bonetti A, Oda K, Kukimoto I, Carninci P, Banks L, Osuga Y, Fujii T. Characterization of novel transcripts of human papillomavirus type 16 using CAGE technology. J Virol. 2015 Feb;89(4):2448-52 PubMed: 25505068

Grison A, Zucchelli S, Urzì A, Zamparo I, Lazarevic D, Pascarella G, Roncaglia P, Giorgetti A, Garcia-Esparcia P, Vlachouli C, Simone R, Persichetti F, Forrest AR, Hayashizaki Y, Carloni P, Ferrer I, Lodovichi C, Plessy C, Carninci P, Gustincich S. Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics. 2014 Aug 27;15(1):729 PubMed: 25164183

Kratz A, Beguin P, Kaneko M, Chimura T, Suzuki AM, Matsunaga A, Kato S, Bertin N, Lassmann T, Vigot R, Carninci P, Plessy C, Launey T. Digital expression profiling of the compartmentalized translatome of Purkinje neurons. Genome Research. 2014 Aug;24(8):1396-410 PubMed: 24904046

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. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature. 2014 Mar 20;507(7492):381-5 PubMed: 24531765

Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, Carninci P, Gustincich S. NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Front Cell Neurosci. 2014 Feb 18;8:41 PubMed: 24600346

Plessy C, Desbois L, Fujii T, Carninci P. Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types. Bioessays. 2013 Feb;35(2):131-40. PubMed: 23281054

Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Zucchelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P. Promoter architecture of mouse olfactory receptor genes. Genome Res. 2012 Mar;22(3):486-97. PubMed: 22194471

Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orlando V, Bell I, Gao H, Dumais J, Kapranov P, Wang H, Davis CA, Gingeras TR, Kawai J, Daub CO, Hayashizaki Y, Gustincich S, Carninci P. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods. 2010 Jul;7(7):528-34 PubMed: 20543846

Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res. 2010 Jun;20(6):791-803 PubMed: 20430781

Biagioli M, Pinto M, Cesselli D, Zaninello M, Lazarevic D, Roncaglia P, Simone R, Vlachouli C, Plessy C, Bertin N, Beltrami A, Kobayashi K, Gallo V, Santoro C, Ferrer I, Rivella S, Beltrami CA, Carninci P, Raviola E, Gustincich S. Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells. Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15454-9 PubMed: 19717439

Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet. 2009 May;41(5):563-71 PubMed: 19377475

Plessy C, Fagiolini M, Wagatsuma A, Harasawa N, Kuji T, Asaka-Oba A, Kanzaki Y, Fujishima S, Waki K, Nakahara H, Hensch TK, Carninci P. A resource for transcriptomic analysis in the mouse brain. PLoS One. 2008 Aug 20;3(8):e3012 PubMed: 18714383

Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, 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 SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006 Jun;38(6):626-35. PubMed: 16645617