RIKEN Center for Integrative Medical Sciences Laboratory for Advanced Genomics Circuit

Team Leader: Jay W. Shin (D.Sc.)

Japanese Page

Research Summary

Human somatic cells have the ability to convert into another cell type by introducing a set of defined factors. These reprogrammed-cells are applicable in regenerative medicine, disease modeling, and drug discovery. My team focuses on the development of key technologies to achieve multitude of cell conversions using both high-throughput robotics and single-cell “multiplex” screening system. These systems integrate with Next Generation Sequencers (NGS) to map the network of mediators, such as transcription factors, noncoding RNAs and epigenetic factors, that are involved in the regulation of (direct) cellular reprogramming.

Main Research Fields

Biological Sciences

Related Research Fields

Biology

Keywords

Single cells
Cell reprogramming
Gene Networks
lncRNA

Selected Publications

1.Tomaru Y, Hasegawa R, Suzuki T, Sato T, Kubosaki A, Suzuki M, Kawaji H, Forrest AR, Hayashizaki Y; FANTOM Consortium, Shin JW, Suzuki H.
"A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation."
Nucleic Acids Res. 42(14), 8905-13 (2014)
2.FANTOM5 Consortium
"A promoter level mammalian expression atlas"
Nature. 507(7493), 462-70 (2014)
3.Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, Forrest AR, Carninci P; FANTOM Consortium.
"Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing."
Genome Res. 24(4), 708-17(2014)
4.Kouno T, de Hoon M, Mar JC, Tomaru Y, Kawano M, Carninci P, Suzuki H, Hayashizaki Y, Shin JW
"Temporal dynamics and transcriptional control using single-cell gene expression analysis."
Genome Biol.? 14(10), R118 (2013)
5.Hasegawa R, Tomaru Y, De Hoon M, Suzuki H, Hayashizaki Y, Shin JW.
"Identification of ZNF395 as a novel modulator of adipogenesis"
Exp Cell Res. 319(3), 68-76 (2013)
6.Shin JW, Suzuki T, Ninomiya N, Kishima M, Hasegawa Y, Kubosaki A, Yabukami H, Suzuki H, Hayashizaki Y.
"stablishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell-reprogramming"
Nucleic Acid Research. 40(21), e165. (2012)
7.Suzuki T, Nakano-Ikegaya M, Yabukami-Okuda H, de Hoon M, Severin J, Saga-Hatano S, Shin JW, Kubosaki A, Simon C, Hasegawa Y, Hayashizaki Y, Suzuki H.
"Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts."
PLoS One 7(3):e33474 (2012)
8.Hasegawa Y, Takahashi N, Forrest AR, Shin JW, Kinoshita Y, Suzuki H, Hayashizaki Y.
"CC chemokine ligand 2 and leukemia inhibitory factor cooperatively promote pluripotency in mouse induced pluripotent cells."
Stem Cells. 29(8), 1196-205 (2011)

Recent Research Results

Apr. 5, 2019
Mapping RNA on a single-cell level

Lab Members

Principal investigator

Jay W. Shin: Team Leader

Core members

Chi Wai Yip: Research Scientist
Divya Sivaraman: Postdoctoral Researcher
Tsukasa Kouno: Research Associate
Youtaro Shibayama: Visiting Scientist
Joachim Luginbuhl: Visiting Researcher

Contact Information

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Email: jay.shin [at] riken.jp