Members

Charles Plessy Mr Charles Plessy, Ph. D.
Senior scientist - Genomics Miniaturization Technology Unit
Phone: 045-503-9219
Email:

Link to OSC Main Activities: FANTOM


Research Interest:

Building on the projects and achievements described below, I am now leading the Genomics Miniaturization Technology Unit in RIKEN's new Center for Life Science Technologies. This page will not be updated anymore; you can follow our work on single cells and population transcriptomics on our new website at the following address.

   http://www-cms.riken.jp/en/research/labs/clst/genom_tech/life_sci_accel/genom_mini/ (in English)

   http://www-cms.riken.jp/research/labs/clst/genom_tech/life_sci_accel/genom_mini/ (in Japanese)

 Population transcriptomics.  We are developing high-troughput methods to profile the transcriptional activity of single cells. My goal is to establish a new field, population transcriptomics, where a biological sample (blood sample, dissociated cells, biopsy, microdissected tissue, etc.) is studied in terms of the population of cell it harbors, grouped by cell types, and the activities of these cells (for instance division, signalling, etc.). In that purpose, I am modifying the nanoCAGE technology that we have developed here, with the aim of 10,000 single cells per sample, that is, up to hundreds of thousands of cells in experimental setups with multiple replicated samples, or millions of cells when aiming at covering a broad number of cell types.


The CAGE method developed at the OSC (see the "Technologies" section of our website) is ideal for studying the regulatory mechanisms that govern cell differentiation and homeostasis, as it focuses on measuring the activity of gene promoters (transcription start sites), in an unbiased way open to the discovery of novel transcripts, with no pre-conceived limit on size, polyadenylation coding potential, etc.  We are excited develop new CAGE protocols to produce data that will question many assumptions that were made when working complex mixtures, which will now isolate in single cells. Among the challenges ahead, there are the definition of gene promoters at the single-cell level, where stochastic transcript counts are expected, or the classification of single-cell profiles of promoter activitiy in overlapping categories extending the classical definitions from cell biology, such as cell type, position in the cell cycle, etc. Our role will be to find the novel and the unexpected at the single-cell resolution.

In parallel, I am also studying T and B lymphocytes by high-troughput sequencing, again with single-cell population transcriptomics as a goal, this time defining the cells by the sequence of their receptors.



Research Project(s):  
Transcriptomic tools to analyse small cell populations.

We are developing nanoCAGE, (Cap Analysis Gene Expression), to analyze transcriptional regulatory networks, promoter usage and gene expression in small biological samples including fixed tissue. The molecular synthesis of sequence tags for the very 5’ ends of both protein coding and noncoding transcripts allows the precise definition of the transcription start sites and the promoters of genes expressed. The decrease of starting materials to as little as 10 ng of total RNA and the increase of sequencing capacity with the second generation sequencing provide a powerful approach to describe gene expression. NanoCAGE is thus suited to provide a comprehensive description of the transcriptome of highly heterogeneous tissues like cancer biopsies or selected brain nuclei.


High-throughput verification of transcriptional starting sites by Deep-RACE.
Biotechniques 2009 Feb;46(2):130-2 Olivarius S, Plessy C, Carninci P
Tunable fractionation of nucleic acids.
Biotechniques 2009 Dec;47(6):1041-3 Salimullah M, Kato S, Murata M, Kawazu C, Plessy C, Carninci P
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
Nat Methods 2010 Jul;7(7):528-34 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
NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes.
Cold Spring Harb Protoc 2011 Jan 1;2011:pdb.prot5559 Salimullah M, Mizuho S, Plessy C, Carninci P
Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
Nucleic Acids Res 2012 Nov 24; Tang DT, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, 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 2012 Dec 27; Plessy C, Desbois L, Fujii T, Carninci P
Transcriptome analysis of small cell populations

We are applying the nanoCAGE technology in collaborative projects, to study various cell types, like purkinje cells, olfactory receptors or dopaminergic neurons.  More recently, I have started a new collaboration to analysse the T cell receptors by sequencing.


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 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
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Genome Res 2010 Jun;20(6):791-803 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
Promoter architecture of mouse olfactory receptor genes.
Genome Res 2011 Dec 22; 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, Succhelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P


Curriculum Vitae:

Molecular biologist and open-source enthousiast. I studied the nervous system of fruit flies and zebrafish in Strasbourg (France) before joining RIKEN for transcriptome-wide studies. I combine experimental and bioinformatics approaches in my work. I am also member of the Debian project, where I keep up-to-date packages related to high-troughput sequence analysis such as BWA, SAMtools, BEDTools, etc. I use Free Software in my research as much as possible, and implement my projects with the same spirit in our workplace, with open lab. wiki, version control repositories, frequent communication and sharing.


Bibliography:

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation.
BMC Genomics 2013 Sep 30;14(1):665 Harbers M, Kato S, de Hoon M, Hayashizaki Y, Carninici P, Plessy C
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 2012 Dec 27; Plessy C, Desbois L, Fujii T, Carninci P
Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
Nucleic Acids Res 2012 Nov 24; Tang DT, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, Carninci P
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
Genome Res 2012 Aug 30; Batut PJ, Dobin A, Plessy C, Carninci P, Gingeras TR
Promoter architecture of mouse olfactory receptor genes.
Genome Res 2011 Dec 22; 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, Succhelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P
RACE: New applications of an old method to connect exons
Tag-based Approaches for Next Generation Sequencing 2011-12-01 Plessy C
NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes.
Cold Spring Harb Protoc 2011 Jan 1;2011:pdb.prot5559 Salimullah M, Mizuho S, Plessy C, Carninci P
Community-driven computational biology with Debian Linux.
BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S5 Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
Nat Methods 2010 Jul;7(7):528-34 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
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Genome Res 2010 Jun;20(6):791-803 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
Tunable fractionation of nucleic acids.
Biotechniques 2009 Dec;47(6):1041-3 Salimullah M, Kato S, Murata M, Kawazu C, Plessy C, Carninci P
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 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
The regulated retrotransposon transcriptome of mammalian cells.
Nat Genet 2009 May;41(5):563-71 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 transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nat Genet 2009 May;41(5):553-62 Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, 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 VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, 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 MC, 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 CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, 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 AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, 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
High-throughput verification of transcriptional starting sites by Deep-RACE.
Biotechniques 2009 Feb;46(2):130-2 Olivarius S, Plessy C, Carninci P
A resource for transcriptomic analysis in the mouse brain.
PLoS One 2008 Aug 20;3(8):e3012 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
Genome-wide analysis of mammalian promoter architecture and evolution.
Nat Genet 2006 Jun;38(6):626-35 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
The complexity of the mammalian transcriptome.
J Physiol 2006 Sep 1;575(Pt 2):321-32 Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P
Genome-wide analysis of mammalian promoter architecture and evolution.
Nat Genet 2006 Jun;38(6):626-35 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
The transcriptional landscape of the mammalian genome.
Science 2005 Sep 2;309(5740):1559-63 Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, 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 SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, 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 KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, 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 SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, 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, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)
Multiple regulatory elements with spatially and temporally distinct activities control neurogenin1 expression in primary neurons of the zebrafish embryo.
Mech Dev 2003 Feb;120(2):211-8 Blader P, Plessy C, Strähle U
Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo.
Genome Res 2004 Feb;14(2):228-38 Dickmeis T, Plessy C, Rastegar S, Aanstad P, Herwig R, Chalmel F, Fischer N, Strähle U
Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes.
Trends Genet 2005 Apr;21(4):207-10 Plessy C, Dickmeis T, Chalmel F, Strähle U