ZFIN ID: ZDB-PERS-010827-9
Plessy, Charles
Email: plessy@riken.jp
URL: http://www.riken.jp/en/research/labs/clst/genom_tech/life_sci_accel/genom_mini/
Address: RIKEN Center for Life Science Technologies Division of Genomic Technologies Genomics Miniaturization Technology Unit 1-7-22 Suehiro-chô, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
Phone: +81-(0)45-503-9222
Fax: +81-(0)45-503-9216
Orcid ID:

Image : Frontal view of a 24h -8.4ngn1:GFP transgenic fish. Nice view on the telencephalon (medial), and on the olfactory bulb (lateral). The dorsalmost structure is the pineal body.

Ph.D. Research Topic: Integration of spatial information by neurogenin1 in zebrafish neural plate.

Current Research Topic: Promotome profiling of large collections of single cells for systems biology.

Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A.M., van IJcken, W.F., Armant, O., Ferg, M., Strähle, U., Carninci, P., Müller, F., and Lenhard, B. (2014) Two independent transcription initiation codes overlap on vertebrate core promoters. Nature. 507(7492):381-385
Plessy, C., Dickmeis, T., Chalmel, F., and Strähle, U. (2005) Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes. Trends Genet.. 21(4):207-210
Blader, P., Lam, C.S., Rastegar, S., Scardigli, R., Nicod, J.C., Simplicio, N., Plessy, C., Fischer, N., Schuurmans, C., Guillemot, F., and Strähle, U. (2004) Conserved and acquired features of neurogenin1 regulation. Development. 131(22):5627-5637
Geling, A., Plessy, C., Rastegar, S., Strähle, U., and Bally-Cuif, L. (2004) Her5 acts as a prepattern factor that blocks neurogenin1 and coe2 expression upstream of Notch to inhibit neurogenesis at the midbrain-hindbrain boundary. Development. 131(9):1993-2006
Dickmeis, T., Plessy, C., Rastegar, S., Aanstad, P., Herwig, R., Chalmel, F., Fischer, N., and Strähle, U. (2004) Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Res.. 14(2):228-238
Blader, P., Plessy, C., and Strähle, U. (2003) Multiple regulatory elements with spatially and temporally distinct activities control neurogenin1 expression in primary neurons of the zebrafish embryo. Mechanisms of Development. 120(2):211-218
Dickmeis, T., Rastegar, S., Aanstad, P., Clark, M., Fischer, N., Plessy, C., Rosa, F., Korzh, V., Strähle, U. (2001) Expression of brain subtype creatine kinase in the zebrafish embryo. Mechanisms of Development. 109(2):409-412


Selected publications on Cap Analysis of Gene Expression and other technologies:

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 (review)

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

Promoter architecture of mouse olfactory receptor genes. 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

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

Salimullah M, Kato S, Murata M, Kawazu C, Plessy C, Carninci P. Tunable fractionation of nucleic acids. Biotechniques. 2009 Dec;47(6):1041-3

Olivarius S, Plessy C, Carninci P. High-throughput verification of transcriptional starting sites by Deep-RACE. Biotechniques. 2009 Feb;46(2):130-2

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.

FANTOM publications:

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

FANTOM Consortium, Suzuki H, et al.. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 2009 May;41(5):553-62

Carninci P, et al.. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006 Jun;38(6):626-635. Epub 2006 Apr 28

The FANTOM Consortium and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). The Transcriptional Landscape of the Mamalian Genome. Science 2005 Sep 2;309(5740):1559-63

On Drosophila:

Van De Bor V, Heitzler P, Leger S, Plessy C, Giangrande A. Precocious expression of the glide/gcm glial-promoting factor in Drosophila induces neurogenesis. Genetics. 2002 Mar;160(3):1095-106