Charles Plessy — Population transcriptomist
My training as a researcher started with developmental genetics in drosophila and zebrafish, where I studied the activity of transcription enhancers (Blader et al., 2003) and their evolutionary conservation (Plessy et al., 2005). This gave me a strong interest for whole-transcriptome analysis and technology. For that purpose, I have joined RIKEN in 2004, where have worked on high-throughput methods for profiling promoters and inferring gene networks, and in particular on CAGE (Cap Analysis Gene Expression).
I have developed a miniaturised 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), benchmarking the use of locked nucleic acids for template switching (Harbers et al., 2013), and reducing the number of primer artefacts and unwanted sequences generated by ribosomal RNAs using low-complexity “pseudo-random” reverse-transcription primers (Arnaud et al., 2016).
On April 2013, I started a new development cycle as the leader of the Genomics Miniaturization Technology Unit at RIKEN Center for Life Sciences, Division of Genomics Technology, to expand this work on single cells following a population transcriptomics approach (Plessy et al., 2013) focused on sampling the largest possible number of cells. In our ongoing developments, we have reached single-cell and single molecule resolution through the introduction of transposase fragmentation and unique molecular identifiers (Poulain et al., 2017). The protocol exists in two versions, one for FACS-isolated cells, and one for the Fluidigm C1 platform (available pre-publication on Fluidigm’s ScriptHub website).
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). To study transcription start activity at nucleotide resolution in zebrafish transfected with chimeric transgenes containing a copy of an endogenous promoter, I combined Deep-RACE, CAGE and paired-end sequencing in a technology that we called “Single-Locus CAGE” (Haberle et al., 2014). 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.
I am also a Free Software enthusiast, and contribute to the Debian Med project, by packaging bioinformatics tools, which are redistributed in Debian (Möller et al., 2010) and its derivatives such as Ubuntu and (cloud)Bio-Linux. For digital signature of my contributions and other activities as a RIKEN researchers, I use the GPG key number B3443334. My ORCID ID is 0000-0001-7410-6295. You can follow me on Mastodon.
Bertin N, Mendez M, Hasegawa A, Lizio M, Abugessaisa I, Severin J, Sakai-Ohno M, Lassmann T, Kasukawa T, Kawaji H, Hayashizaki Y, Forrest ARR, Carninci P, Plessy C✉. Linking FANTOM5 CAGE peaks to annotations with CAGEscan. Sci Data. 2017 Oct 3;4:170147 PubMed: 28972578
Poulain S, Kato S, Arnaud O, Morlighem JÉ, Suzuki M, Plessy C✉, Harbers M✉. NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes. Methods Mol Biol. 2017 1543:57-109 PubMed: 28349422
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
Abdelhamid RF☮, Plessy C☮, Yamauchi Y, Taoka M, de Hoon M, Gingeras TR, Isobe T, Carninci P. Multiplicity of 5′ Cap Structures Present on Short RNAs. PLOS ONE. 2014 Jul 31;9(7):e102895 PubMed: 25079783
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
Harbers M, Kato S, de Hoon M, Hayashizaki Y, Carninci P, Plessy C. 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. PubMed: 24079827
Tang DT, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, Carninci P. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching. Nucleic Acids Res. 2013 Feb 1;41(3):e44. PubMed: 23180801
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
Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res. 2013 Jan;23(1):169-80. PubMed: 22936248
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
Bertin N, Plessy C, Carninci P, Harbers M. Definition of Promotome–Transcriptome Architecture Using CAGEscan. 2012. Chapter 3 in in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany.
Plessy C. RACE: New Applications of an Old Method to Connect Exons. 2012. Chapter 4 in in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany.
Salimullah M, Sakai M, Plessy C, Carninci P. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harb Protoc. 2011 Jan 1;2011(1):pdb.prot5559. PubMed: 21205859
Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C. Community-driven computational biology with Debian Linux. BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S5. PubMed: 21210984
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
Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P✉. The complexity of the mammalian transcriptome. Review J Physiol. 2006 Sep 1;575(Pt 2):321-32. PubMed: 16857706
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